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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE SCYALONE DEHYDRATASE (YP_496742.1) FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 AT 1.50 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  08 Sep 08  (Deposition) - 30 Sep 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  B  (3x)
Keywords :  Yp_496742. 1, Putative Scyalone Dehydratase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Unknown Function, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Scyalone Dehydratase (Yp_496742. 1) From Novosphingobium Aromaticivorans Dsm 12444 At 1. 50 A Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE SCYALONE DEHYDRATASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YP_496742.1, SARO_1465
    Organism Scientific: NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444
    Organism Taxid: 279238

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): A 
Biological Unit 2 (3x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 26)

Asymmetric Unit (5, 26)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2MSE12Mod. Amino AcidSELENOMETHIONINE
3PEG5Ligand/IonDI(HYDROXYETHYL)ETHER
4PG44Ligand/IonTETRAETHYLENE GLYCOL
5PGE4Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (4, 42)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MSE18Mod. Amino AcidSELENOMETHIONINE
3PEG9Ligand/IonDI(HYDROXYETHYL)ETHER
4PG43Ligand/IonTETRAETHYLENE GLYCOL
5PGE12Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 2 (3, 33)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MSE18Mod. Amino AcidSELENOMETHIONINE
3PEG6Ligand/IonDI(HYDROXYETHYL)ETHER
4PG49Ligand/IonTETRAETHYLENE GLYCOL
5PGE-1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:196 , HOH A:220BINDING SITE FOR RESIDUE MG A 150
02AC2SOFTWAREARG A:97 , THR A:132BINDING SITE FOR RESIDUE PEG A 151
03AC3SOFTWAREARG A:14 , ASP A:79 , GLN A:121 , LYS B:100BINDING SITE FOR RESIDUE PEG A 152
04AC4SOFTWAREGLU A:101BINDING SITE FOR RESIDUE PEG A 153
05AC5SOFTWAREASP B:79 , ASN B:87 , VAL B:88 , PHE B:112 , ASP B:113 , HOH B:218BINDING SITE FOR RESIDUE PEG B 150
06AC6SOFTWAREGLU B:8 , GLU B:83BINDING SITE FOR RESIDUE PEG B 151
07AC7SOFTWAREVAL A:7 , GLU A:8 , ALA A:11 , LYS A:117 , HOH A:195 , HOH A:206 , HOH A:219BINDING SITE FOR RESIDUE PGE A 154
08AC8SOFTWAREASP A:38 , GLU A:40 , GLU A:85 , LYS A:125BINDING SITE FOR RESIDUE PGE A 155
09AC9SOFTWAREARG A:14 , CYS A:77 , ASP A:79 , ASN A:87 , VAL A:88 , ARG A:89 , ASP A:113BINDING SITE FOR RESIDUE PGE A 156
10BC1SOFTWAREASN A:5 , VAL A:7 , MSE A:9 , ARG A:10 , ARG A:14 , CYS A:77 , ILE A:78 , HOH A:180BINDING SITE FOR RESIDUE PGE A 157
11BC2SOFTWAREARG B:67 , ARG B:97 , THR B:131 , THR B:132 , THR B:134 , ARG B:140 , HOH B:180BINDING SITE FOR RESIDUE PG4 B 152
12BC3SOFTWAREGLU A:101 , ARG A:102 , PRO A:103 , ASP A:104 , HOH A:204 , HOH A:243BINDING SITE FOR RESIDUE PG4 A 158
13BC4SOFTWAREARG B:130 , PRO B:144 , ILE B:145 , GLY B:146 , ARG B:147 , HOH B:175 , HOH B:199 , HOH B:201BINDING SITE FOR RESIDUE PG4 B 153
14BC5SOFTWAREARG B:102 , PRO B:103 , ASP B:104 , HOH B:217BINDING SITE FOR RESIDUE PG4 B 154

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EF8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3EF8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EF8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EF8)

(-) Exons   (0, 0)

(no "Exon" information available for 3EF8)

(-) 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:149
 aligned with Q2G8B5_NOVAD | Q2G8B5 from UniProtKB/TrEMBL  Length:149

    Alignment length:149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         
         Q2G8B5_NOVAD     1 MTDTNLVEMRAIERMMFDYSYHLDMNHPEELAALFVEDCEVSYAPNFGATGRDAYKKTLEGIGTFFRGTSHHNSNICIDFVSETEANVRSVVLAIHRYTKERPDGILYGQYFDTVVKVDGQWKFKRRELRTTMTTDYHVRAANPIGRAE 149
               SCOP domains d3ef8a1 A:1-149 Uncharacterized protein Saro1465                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.eeeeeeeeee..eeeehhhhhhhhh.hhhhheeeeeeeeeeeeeeeee..eeeeeeeeeeeeee......eeeeeeeeeeeeee..eeeeeeeeeeeeeee.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ef8 A   1 mTDTNLVEmRAIERmmFDYSYHLDmNHPEELAALFVEDCEVSYAPNFGATGRDAYKKTLEGIGTFFRGTSHHNSNICIDFVSETEANVRSVVLAIHRYTKERPDGILYGQYFDTVVKVDGQWKFKRRELRTTmTTDYHVRAANPIGRAE 149
                            |       10    ||  20    |   30        40        50        60        70        80        90       100       110       120       130  |    140         
                            |       9-MSE ||       25-MSE                                                                                                     133-MSE            
                            1-MSE        15-MSE                                                                                                                                  
                                          16-MSE                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:149
 aligned with Q2G8B5_NOVAD | Q2G8B5 from UniProtKB/TrEMBL  Length:149

    Alignment length:149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         
         Q2G8B5_NOVAD     1 MTDTNLVEMRAIERMMFDYSYHLDMNHPEELAALFVEDCEVSYAPNFGATGRDAYKKTLEGIGTFFRGTSHHNSNICIDFVSETEANVRSVVLAIHRYTKERPDGILYGQYFDTVVKVDGQWKFKRRELRTTMTTDYHVRAANPIGRAE 149
               SCOP domains d3ef8b_ B: Uncharacterized protein Saro1465                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.eeeeeeeeee..eeeehhhhhhhhh.hhhhheeeeeeeeeeeeeeeee..eeeeeeeeeeeeee......eeeeeeeeeeeeee..eeeeeeeeeeeeeee.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ef8 B   1 mTDTNLVEmRAIERmmFDYSYHLDmNHPEELAALFVEDCEVSYAPNFGATGRDAYKKTLEGIGTFFRGTSHHNSNICIDFVSETEANVRSVVLAIHRYTKERPDGILYGQYFDTVVKVDGQWKFKRRELRTTmTTDYHVRAANPIGRAE 149
                            |       10    ||  20    |   30        40        50        60        70        80        90       100       110       120       130  |    140         
                            1-MSE   9-MSE ||       25-MSE                                                                                                     133-MSE            
                                         15-MSE                                                                                                                                  
                                          16-MSE
   Legend:   → Mismatch (orange background)
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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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3EF8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EF8)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3EF8)

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