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(-) Description

Title :  HIGH RESOLUTION STRUCTURE OF 3-HYDROXYDECANOYL-(ACYL CARRIER PROTEIN) DEHYDRATASE FROM YERSINIA PESTIS AT 1.35 A
 
Authors :  C. Chang, N. Maltseva, Y. Kim, R. Mulligan, K. Kwon, W. F. Anderson, A. Jo Center For Structural Genomics Of Infectious Diseases (Csgi
Date :  04 Jan 16  (Deposition) - 20 Jan 16  (Release) - 20 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,G  (1x)
Biol. Unit 2:  B,F  (1x)
Biol. Unit 3:  C,E  (1x)
Biol. Unit 4:  D,H  (1x)
Keywords :  Structural Genomics, Psi-Biology, Midwest Center For Structural Genomics, Mcsg, Center For Structural Genomics Of Infectious Diseases, Csgid, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Chang, N. Maltseva, Y. Kim, R. Mulligan, K. Kwon, W. F. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
High Resolution Structure Of 3-Hydroxydecanoyl-(Acyl Carrie Protein) Dehydratase From Yersinia Pestis At 1. 35 A
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
    Chains: A, B, C, D, E, F, G, H
    EC Number: 4.2.1.59
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Taxid: 562
    Gene: FABA, AK38_1122
    Organism Scientific: YERSINIA PESTIS CO92
    Organism Taxid: 214092
    Synonym: 3-HYDROXYACYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE FABA,BETA- HYDROXYDECANOYL THIOESTER DEHYDRASE,TRANS-2-DECENOYL-[ACYL-CARRIER- PROTEIN] ISOMERASE

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): A     G 
Biological Unit 2 (1x):  B   F  
Biological Unit 3 (1x):   C E   
Biological Unit 4 (1x):    D   H

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 85)

Asymmetric Unit (2, 85)
No.NameCountTypeFull Name
1GOL15Ligand/IonGLYCEROL
2MSE70Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 20)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2MSE17Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 20)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2MSE17Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 22)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MSE18Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (2, 23)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2MSE18Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMSE A:78 , GLY A:80 , GLY A:116 , GLN A:117 , TYR A:156 , HOH A:322 , ARG G:105 , ALA G:106 , PHE G:172 , GOL G:202binding site for residue GOL A 201
02AC2SOFTWAREMSE B:78 , GLY B:80 , GLY B:116 , GLN B:117 , TYR B:156 , HOH B:315 , HOH B:322 , ARG F:105 , ALA F:106 , PHE F:172binding site for residue GOL B 201
03AC3SOFTWAREMSE C:78 , GLY C:80 , GLY C:116 , GLN C:117 , TYR C:156 , HOH C:319 , ARG E:105 , ALA E:106 , PHE E:172 , HOH E:303binding site for residue GOL C 201
04AC4SOFTWARELYS C:138 , LEU C:165 , LYS C:167 , ASP C:168 , HOH C:303 , HOH C:361binding site for residue GOL C 202
05AC5SOFTWAREARG C:105 , ALA C:106 , MSE E:78 , PRO E:79 , GLY E:80 , GLY E:116 , GLN E:117 , TYR E:156 , HOH E:328binding site for residue GOL C 203
06AC6SOFTWAREARG D:133 , ASP D:160 , LYS D:162 , HOH D:305 , LYS H:10 , GLU H:11binding site for residue GOL D 201
07AC7SOFTWAREMSE D:78 , GLY D:80 , GLY D:116 , GLN D:117 , TYR D:156 , HOH D:318 , ARG H:105 , ALA H:106 , PHE H:172 , GOL H:202binding site for residue GOL D 202
08AC8SOFTWAREPHE C:72 , PRO E:30 , TRP E:88 , GLN E:89 , GLY E:104 , HOH E:303 , HOH E:318 , HOH E:337binding site for residue GOL E 201
09AC9SOFTWAREARG B:105 , ALA B:106 , HOH B:448 , MSE F:78 , GLY F:80 , GLY F:116 , GLN F:117 , TYR F:156 , HOH F:329binding site for residue GOL F 201
10AD1SOFTWAREPHE B:72 , HOH B:315 , TRP F:88 , GLN F:89 , VAL F:163 , HOH F:334 , HOH F:356binding site for residue GOL F 202
11AD2SOFTWAREARG A:105 , ALA A:106 , MSE G:78 , GLY G:80 , GLY G:116 , GLN G:117 , TYR G:156 , HOH G:338binding site for residue GOL G 201
12AD3SOFTWAREPHE A:72 , GOL A:201 , PRO G:30 , ASP G:85 , TRP G:88 , GLN G:89 , GLY G:104 , ARG G:105 , ALA G:106 , HOH G:307 , HOH G:311binding site for residue GOL G 202
13AD4SOFTWAREARG D:105 , ALA D:106 , MSE H:78 , GLY H:80 , GLY H:116 , GLN H:117 , TYR H:156 , HOH H:329 , HOH H:412binding site for residue GOL H 201
14AD5SOFTWAREPHE D:72 , GOL D:202 , TRP H:88 , ALA H:106 , HOH H:321 , HOH H:345binding site for residue GOL H 202
15AD6SOFTWARELYS H:10 , GLY H:32 , LEU H:35 , ASP H:38 , LEU H:59 , LEU H:65 , HOH H:333 , HOH H:359 , HOH H:368binding site for residue GOL H 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5HD6)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1His A:71 -Phe A:72
2His B:71 -Phe B:72
3His C:71 -Phe C:72
4His D:71 -Phe D:72
5His E:71 -Phe E:72
6His F:71 -Phe F:72
7His G:71 -Phe G:72
8His H:71 -Phe H:72

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HD6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HD6)

(-) Exons   (0, 0)

(no "Exon" information available for 5HD6)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhh............hhhhh...eeeeee.........eeeeeee....hhhhhhh.......hhhhhhhhhhhhhhhhhhhh....eeeeeee.eeee.........eeeeeeeeeeeee...eeeeeeeeeee..eeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hd6 A  -2 SNAmVDKRESYTKEDLEASGRGELFGAGGPPLPAGNmLmmDRIVKmIEDGGSHNKGYVEAELDINPDLWFFGCHFIGDPVmPGCLGLDAmWQLVGFYLGWLGGEGKGRALGVGEVKFTGQVLPDAKKVTYRINFKRVImRKLImGVADGEVLVDGKVIYTATDLKVGLFKDTNAF 172
                               |     7        17        27      | 37     |  47        57        67        77|       87        97       107       117       127       137   |   147       157       167     
                               |                               34-MSE    |                                 78-MSE   87-MSE                                          136-MSE|                               
                               1-MSE                             36-MSE  |                                                                                               141-MSE                           
                                                                  37-MSE |                                                                                                                                 
                                                                        43-MSE                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhh............hhhhh...eeeeee.........eeeeeee....hhhhhhh.......hhhhhhhhhhhhhhhhhhhh....eeeeeee.eeee.........eeeeeeeeeeeee...eeeeeeeeeee..eeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hd6 B  -2 SNAmVDKRESYTKEDLEASGRGELFGAGGPPLPAGNmLmmDRIVKmIEDGGSHNKGYVEAELDINPDLWFFGCHFIGDPVmPGCLGLDAmWQLVGFYLGWLGGEGKGRALGVGEVKFTGQVLPDAKKVTYRINFKRVImRKLImGVADGEVLVDGKVIYTATDLKVGLFKDTNAF 172
                               |     7        17        27      | 37     |  47        57        67        77|       87        97       107       117       127       137   |   147       157       167     
                               1-MSE                           34-MSE    |                                 78-MSE   87-MSE                                          136-MSE|                               
                                                                 36-MSE  |                                                                                               141-MSE                           
                                                                  37-MSE |                                                                                                                                 
                                                                        43-MSE                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhh............hhhhh...eeeeee.........eeeeeee....hhhhhhh.......hhhhhhhhhhhhhhhhhhhh....eeeeeee.eeee.........eeeeeeeeeeeee...eeeeeeeeeee..eeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hd6 C  -2 SNAmVDKRESYTKEDLEASGRGELFGAGGPPLPAGNmLmmDRIVKmIEDGGSHNKGYVEAELDINPDLWFFGCHFIGDPVmPGCLGLDAmWQLVGFYLGWLGGEGKGRALGVGEVKFTGQVLPDAKKVTYRINFKRVImRKLImGVADGEVLVDGKVIYTATDLKVGLFKDTNAF 172
                               |     7        17        27      | 37     |  47        57        67        77|       87        97       107       117       127       137   |   147       157       167     
                               1-MSE                           34-MSE    |                                 78-MSE   87-MSE                                          136-MSE|                               
                                                                 36-MSE  |                                                                                               141-MSE                           
                                                                  37-MSE |                                                                                                                                 
                                                                        43-MSE                                                                                                                             


Chain D from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhh............hhhhh...eeeeee.........eeeeeee....hhhhhhh.......hhhhhhhhhhhhhhhhhhhh....eeeeeee.eeee.........eeeeeeeeeeeee...eeeeeeeeeee..eeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hd6 D  -2 SNAmVDKRESYTKEDLEASGRGELFGAGGPPLPAGNmLmmDRIVKmIEDGGSHNKGYVEAELDINPDLWFFGCHFIGDPVmPGCLGLDAmWQLVGFYLGWLGGEGKGRALGVGEVKFTGQVLPDAKKVTYRINFKRVImRKLImGVADGEVLVDGKVIYTATDLKVGLFKDTNAF 172
                               |     7        17        27      | 37     |  47        57        67        77|       87        97       107       117       127       137   |   147       157       167     
                               1-MSE                           34-MSE    |                                 78-MSE   87-MSE                                          136-MSE|                               
                                                                 36-MSE  |                                                                                               141-MSE                           
                                                                  37-MSE |                                                                                                                                 
                                                                        43-MSE                                                                                                                             


Chain E from PDB  Type:PROTEIN  Length:173
                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhh............hhhhh...eeeeee.........eeeeeee....hhhhhhh.......hhhhhhhhhhhhhhhhhhhh....eeeeeee..eee.........eeeeeeeeeeeee...eeeeeeeeeee..eeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hd6 E   0 AmVDKRESYTKEDLEASGRGELFGAGGPPLPAGNmLmmDRIVKmIEDGGSHNKGYVEAELDINPDLWFFGCHFIGDPVmPGCLGLDAmWQLVGFYLGWLGGEGKGRALGVGEVKFTGQVLPDAKKVTYRINFKRVImRKLImGVADGEVLVDGKVIYTATDLKVGLFKDTNAF 172
                             |       9        19        29    | ||39   |    49        59        69        79       |89        99       109       119       129      |139 |     149       159       169   
                             1-MSE                           34-MSE    |                                 78-MSE   87-MSE                                          136-MSE|                               
                                                               36-MSE  |                                                                                               141-MSE                           
                                                                37-MSE |                                                                                                                                 
                                                                      43-MSE                                                                                                                             


Chain F from PDB  Type:PROTEIN  Length:168
                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhh............hhhhh...eeeeee.........eeeeeee....hhhhhhh.......hhhhhhhhhhhhhhhhhhhh....eeeeeee..eee.........eeeeeeeeeeeee...eeeeeeeeeee..eeeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5hd6 F   3 DKRESYTKEDLEASGRGELFGAGGPPLPAGNmLmmDRIVKmIEDGGSHNKGYVEAELDINPDLWFFGCHFIGDPVmPGCLGLDAmWQLVGFYLGWLGGEGKGRALGVGEVKFTGQVLPDAKKVTYRINFKRVImRKLImGVADGEVLVDGKVIYTATDLKVGLFKDTF 172
                                    12        22        32 | ||   42|       52        62        72     |  82    |   92       102       112       122       132   |   142       152       162      ||
                                                          34-MSE    |                                 78-MSE   87-MSE                                          136-MSE|                         169|
                                                            36-MSE  |                                                                                               141-MSE                      172
                                                             37-MSE |                                                                                                                               
                                                                   43-MSE                                                                                                                           


Chain G from PDB  Type:PROTEIN  Length:168
                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhh............hhhhh...eeeeee.........eeeeeee....hhhhhhh.......hhhhhhhhhhhhhhhhhhhh....eeeeeee..eee.........eeeeeeeeeeeee...eeeeeeeeeee..eeeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5hd6 G   3 DKRESYTKEDLEASGRGELFGAGGPPLPAGNmLmmDRIVKmIEDGGSHNKGYVEAELDINPDLWFFGCHFIGDPVmPGCLGLDAmWQLVGFYLGWLGGEGKGRALGVGEVKFTGQVLPDAKKVTYRINFKRVImRKLImGVADGEVLVDGKVIYTATDLKVGLFKDTF 172
                                    12        22        32 | ||   42|       52        62        72     |  82    |   92       102       112       122       132   |   142       152       162      ||
                                                          34-MSE    |                                 78-MSE   87-MSE                                          136-MSE|                         169|
                                                            36-MSE  |                                                                                               141-MSE                      172
                                                             37-MSE |                                                                                                                               
                                                                   43-MSE                                                                                                                           


Chain H from PDB  Type:PROTEIN  Length:172
                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhh............hhhhh...eeeeee.........eeeeeee....hhhhhhh.......hhhhhhhhhhhhhhhhhhhh....eeeeeee..eee.........eeeeeeeeeeeee...eeeeeeeeeee..eeeeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hd6 H   0 AmVDKRESYTKEDLEASGRGELFGAGGPPLPAGNmLmmDRIVKmIEDGGSHNKGYVEAELDINPDLWFFGCHFIGDPVmPGCLGLDAmWQLVGFYLGWLGGEGKGRALGVGEVKFTGQVLPDAKKVTYRINFKRVImRKLImGVADGEVLVDGKVIYTATDLKVGLFKDTNF 172
                             |       9        19        29    | ||39   |    49        59        69        79       |89        99       109       119       129      |139 |     149       159       169||
                             |                               34-MSE    |                                 78-MSE   87-MSE                                          136-MSE|                          170|
                             1-MSE                             36-MSE  |                                                                                               141-MSE                       172
                                                                37-MSE |                                                                                                                                
                                                                      43-MSE
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5HD6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HD6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HD6)

(-) Gene Ontology  (10, 10)

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        FABA_YERPE | Q8ZG80: 5f6r

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