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(-) Description

Title :  CRYSTAL STRUCTURE OF PERIPLASMIC BINDING PROTEIN TYPE 1 FROM BORDETELLA PERTUSSIS TOHAMA I COMPLEXED WITH 3-HYDROXY BENZOIC ACID
 
Authors :  Y. Kim, G. Joachimiak, S. Clancy, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  23 Apr 14  (Deposition) - 02 Jul 14  (Release) - 02 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Psi-Biology, Midwest Center For Structural Genomics, Mcsg, Alpha-Beta Fold, Sbp, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, G. Joachimiak, S. Clancy, A. Joachimiak
Crystal Structure Of Periplasmic Binding Protein Type 1 Fro Bordetella Pertussis Tohama I Complexed With 3-Hydroxy Benzoic Acid
To Be Published 2014
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE LEU/ILE/VAL-BINDING PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG68
    Expression System Strain: BL21(DE3) GOLD
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BP0622
    Organism Scientific: BORDETELLA PERTUSSIS
    Organism Taxid: 257313
    Strain: TOHAMA I
    Synonym: PERIPLASMIC BINDING PROTEIN TYPE I

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 33)

Asymmetric Unit (5, 33)
No.NameCountTypeFull Name
13HB2Ligand/Ion3-HYDROXYBENZOIC ACID
2EDO4Ligand/Ion1,2-ETHANEDIOL
3GOL2Ligand/IonGLYCEROL
4MSE24Mod. Amino AcidSELENOMETHIONINE
5SO41Ligand/IonSULFATE ION
Biological Unit 1 (4, 18)
No.NameCountTypeFull Name
13HB1Ligand/Ion3-HYDROXYBENZOIC ACID
2EDO3Ligand/Ion1,2-ETHANEDIOL
3GOL2Ligand/IonGLYCEROL
4MSE12Mod. Amino AcidSELENOMETHIONINE
5SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (4, 15)
No.NameCountTypeFull Name
13HB1Ligand/Ion3-HYDROXYBENZOIC ACID
2EDO1Ligand/Ion1,2-ETHANEDIOL
3GOL-1Ligand/IonGLYCEROL
4MSE12Mod. Amino AcidSELENOMETHIONINE
5SO41Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:44 , GLY A:106 , SER A:107 , ILE A:128 , ALA A:129 , GLN A:130 , TYR A:183 , LEU A:236 , GLY A:261 , ILE A:324 , HOH A:623BINDING SITE FOR RESIDUE 3HB A 501
2AC2SOFTWAREASN A:156 , GLU A:159 , ALA A:160 , GLY A:187 , LEU A:191 , SER A:259 , HOH A:632BINDING SITE FOR RESIDUE GOL A 502
3AC3SOFTWAREILE A:65 , ASN A:66 , ILE A:340 , ASN A:344 , SER A:345BINDING SITE FOR RESIDUE EDO A 503
4AC4SOFTWAREALA A:205 , THR A:206 , ARG A:222BINDING SITE FOR RESIDUE EDO A 504
5AC5SOFTWARETRP A:59 , LYS A:62 , HOH A:639BINDING SITE FOR RESIDUE EDO A 505
6AC6SOFTWAREGLU A:338 , ARG A:341 , LEU A:342 , LYS A:359 , HOH A:660 , HOH A:777 , HOH A:823BINDING SITE FOR RESIDUE GOL A 506
7AC7SOFTWAREPHE B:44 , GLY B:106 , SER B:107 , ILE B:128 , ALA B:129 , GLN B:130 , TYR B:183 , LEU B:236 , GLY B:261 , ILE B:324 , HOH B:623BINDING SITE FOR RESIDUE 3HB B 501
8AC8SOFTWAREARG A:245 , ARG A:249 , ARG B:245 , ARG B:249 , HOH B:678BINDING SITE FOR RESIDUE SO4 B 502
9AC9SOFTWAREILE B:65 , ASN B:66 , LYS B:68 , ILE B:340 , ASN B:344 , SER B:345BINDING SITE FOR RESIDUE EDO B 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q6W)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:288 -Pro A:289
2Asn B:288 -Pro B:289

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q6W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q6W)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q6W)

(-) 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:376
                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.....hhhhhhhhhhhhhhhhhhhhhh.......eeeeeeee...hhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhh..eee....hhhhh.............eee...hhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhh......eeeee......hhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh....ee....ee..........hhh.eeeeeeeee..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q6w A  26 ADTIKIGmTSALTGPYNEFGEGNRRAVELAVEQWNAKGGINGKKIEIAmLLDDQLNPDRAVQNIRAILDNKDIVGIIGPAGSGPmLAVIDmVQADGRPYmNPIAQTPVVTYPGEKTGEKPRPNVFSFALQNDIEAVAmGEYLAKKFKRVGIIHESTAYGVTGVDYLAASIAKNGGAKPVATDSYNQGAQDmTAQVARmKRANVDAIAAIGLGKDLAVLRRTmARLNVNVPLAASNGALGQPYQEGAGELTLGTLGTmIGAFGNPmRAPAADFAKAYKAKYGTDRWWGNDPENPQLFmAISVSNGYDAANILFEGIRLANSTDPKAVIAAIESIKDYQGVNTAYTFSKERHHGIETDGVKVFEYVKKGDKIRLEPIA 401
                                   |35        45        55        65        75        85        95       105    |  115|      125       135       145       155       165       175       185       195       205       215|      225       235       245 |     255       265       275      |285    |  295       305       315      |325       335       345       355       365       375       385       395      
                                  33-MSE                                   74-MSE                             110-MSE |      125-MSE                               163-MSE                                              216-MSE  |                     247-MSE                            282-MSE 290-MSE                         322-MSE                                                                           
                                                                                                                    116-MSE                                                                                                    223-MSE                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:376
                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.....hhhhhhhhhhhhhhhhhhhhhh.......eeeeeeee...hhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh..eee....hhhhh.............eee...hhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhh......eeeee......hhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhhhhh.eeeeee.......hhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh....ee....ee..........hhh.eeeeeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q6w B  25 AADTIKIGmTSALTGPYNEFGEGNRRAVELAVEQWNAKGGINGKKIEIAmLLDDQLNPDRAVQNIRAILDNKDIVGIIGPAGSGPmLAVIDmVQADGRPYmNPIAQTPVVTYPGEKTGEKPRPNVFSFALQNDIEAVAmGEYLAKKFKRVGIIHESTAYGVTGVDYLAASIAKNGGAKPVATDSYNQGAQDmTAQVARmKRANVDAIAAIGLGKDLAVLRRTmARLNVNVPLAASNGALGQPYQEGAGELTLGTLGTmIGAFGNPmRAPAADFAKAYKAKYGTDRWWGNDPENPQLFmAISVSNGYDAANILFEGIRLANSTDPKAVIAAIESIKDYQGVNTAYTFSKERHHGIETDGVKVFEYVKKGDKIRLEPI 400
                                    34        44        54        64        74        84        94       104     | 114 |     124|      134       144       154       164       174       184       194       204       214 |     224       234       244  |    254       264       274       284     | 294       304       314       324       334       344       354       364       374       384       394      
                                   33-MSE                                   74-MSE                             110-MSE |      125-MSE                               163-MSE                                              216-MSE  |                     247-MSE                            282-MSE 290-MSE                         322-MSE                                                                          
                                                                                                                     116-MSE                                                                                                    223-MSE
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  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 4Q6W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q6W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q6W)

(-) Gene Ontology  (1, 1)

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(-) Related Entries Specified in the PDB File

4mpt THE SAME PROTEIN WITHOUT LIGAND RELATED ID: MCSG-APC110230 RELATED DB: TARGETTRACK