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(-) Description

Title :  CRYSTAL STRUCTURE OF TOLB PROTEIN FROM YERSINIA PESTIS CO92
 
Authors :  N. Maltseva, Y. Kim, J. Osipiuk, W. F. Anderson, A. Joachimiak, Center Structural Genomics Of Infectious Diseases (Csgid)
Date :  21 Mar 14  (Deposition) - 02 Apr 14  (Release) - 02 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Niaid, National Institute Of Allergy And Infectious Diseases, Center For Structural Genomics Of Infectious Diseases, Csgid, Alpha-Beta Fold And Beta Propeller Fold, Translocation, Pal, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Maltseva, Y. Kim, J. Osipiuk, W. F. Anderson, A. Joachimiak
Crystal Structure Of Tolb Protein From Yersinia Pestis Co92
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROTEIN TOLB
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG68
    Expression System Strain: BL21 MAGIC
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 23-430
    Gene: TOLB, Y3055, YPO1124, YP_1032
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 214092
    Strain: CO92

 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, 16)

Asymmetric Unit (5, 16)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3MSE11Mod. Amino AcidSELENOMETHIONINE
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
5SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MES-1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3MSE5Mod. Amino AcidSELENOMETHIONINE
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (5, 10)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3MSE6Mod. Amino AcidSELENOMETHIONINE
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5SO41Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:65 , PHE A:153 , GLY A:161 , ALA A:162 , PHE A:163 , TYR A:187 , ASN A:385 , THR A:387 , MSE A:388 , HOH A:810BINDING SITE FOR RESIDUE PEG A 501
2AC2SOFTWAREGLN A:139 , ARG A:166 , ASP A:186 , ASN A:191 , GLN B:139 , TRP B:140 , HOH B:603 , HOH B:664BINDING SITE FOR RESIDUE GOL B 501
3AC3SOFTWAREARG A:166 , PHE A:193 , LEU A:231 , TRP B:140 , SO4 B:503 , HOH B:654 , HOH B:700 , HOH B:765BINDING SITE FOR RESIDUE MES B 502
4AC4SOFTWAREARG B:166 , LEU B:231 , MES B:502 , HOH B:644 , HOH B:704BINDING SITE FOR RESIDUE SO4 B 503
5AC5SOFTWAREPHE B:153 , GLY B:161 , ALA B:162 , PHE B:163 , TYR B:187 , ASN B:385 , THR B:387 , MSE B:388 , HOH B:742BINDING SITE FOR RESIDUE PEG B 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4PWZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PWZ)

(-) 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:405
                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4pwza1 A:23-161 automated matches                                                                                                         d4pwza2 A:162-430 automated matches                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....eeeee...ee........hhhhhhhhhhhhh..eee.hhhhh.....hhhhhhhhhhhh....eeeeeeeee.....eeeeeeeee......eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhh.......eeeeeee.......eeeeeee......eeeeee...eeeeee.....eeeeee.....eeeeeee.....eeeeeee....eeeee.....eeeeee......eeeeee.....eee.......eeeeee.....eeeeee......eeeeee......ee......eeeeeee.....eeeeeee..eeeeee.....eee....eeeeeeee.....eeeeeeee..eeeeeeee.....eee......eeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pwz A  23 VRIEITQGVDSARPIGVVPFKWmGPGTPPEEIGAIVGADLRNSGKFNPIDAARmPQQPSTAAEVTPAAWTALGIDAVVVGQVQPSADGSYVVSYQLVDTSGSAGSILAQNQYKVTKQWLRYSAHTVSDEVFEKLTGIKGAFRTRIAYVVKTNGGKFPHELRVSDYDGYNQFVVHRSPEPLmSPAWSPDGSKIAYVTFESGKSALVIQTLANGAIRQVASFPRHNGAPAFSPDGTKLAFALSKSGSLNLYVmDLASGQISQVTDGRSNNTEPSWFPDSQNLAYTSDQGGRPQVYKVNINGGVPQRITWEGSQNQNADVSPDGKFLVLVSSAQHIAKQDLETGAVQVLTDTLLDETPSIAPNGTmVIYSSTQGLGSVLQLVSTDGRFKARLPATDGQVKFPAWSPYL 430
                                    32        42  |     52        62        72   |    82        92       102       112       122       132       142       152       162       172       182       192       202|      212       222       232       242       252       262       272|      282       292       302       312       322       332       342       355       365       375       385  |    395       405       415       425     
                                                 45-MSE                         76-MSE                                                                                                                        203-MSE                                                               273-MSE                                                                       351|                              388-MSE                                      
                                                                                                                                                                                                                                                                                                                                                                   355                                                                           


Chain B from PDB  Type:PROTEIN  Length:406
                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4pwzb1 B:1-161 automated matches                                                                                                           d4pwzb2 B:162-430 automated matches                                                                                                                                                                                                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.....eeeee...ee........hhhhhhhhhhhhh..eee.hhhhh.....hhhhhhhhhhhh....eeeeeeeee.....eeeeeeeee......eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhh.......eeeeeee.......eeeeeee......eeeeee...eeeeee.....eeeeee.....eeeeeee.....eeeeeee....eeeee.....eeeeee......eeeeee.....eee.......eeeeee.....eeeeee......eeeeee......ee.......eeeeee.....eeeeee...eeeeee.....eee.......eeeee.....eeeeeeee..eeeeeeee.....eee......eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pwz B   1 mVRIEITQGVDSARPIGVVPFKWmGPGTPPEEIGAIVGADLRNSGKFNPIDAARmPQQPSTAAEVTPAAWTALGIDAVVVGQVQPSADGSYVVSYQLVDTSGSAGSILAQNQYKVTKQWLRYSAHTVSDEVFEKLTGIKGAFRTRIAYVVKTNGGKFPHELRVSDYDGYNQFVVHRSPEPLmSPAWSPDGSKIAYVTFESGKSALVIQTLANGAIRQVASFPRHNGAPAFSPDGTKLAFALSKSGSLNLYVmDLASGQISQVTDGRSNNTEPSWFPDSQNLAYTSDQGGRPQVYKVNINGGVPQRITWEGSQNQNADVSPDGKFLVLVSSAQHIAKQDLETGAVQVLTDTLLDETPSIAPNGTmVIYSSTQGLGSVLQLVSTDGRFKARLPATDGQVKFPAWSPYL 430
                            ||      31        41   |    51        61        71    |   81        91       101       111       121       131       141       151       161       171       181       191       201 |     211       221       231       241       251       261       271 |     281       291       301       311       321       331       341       351|      364       374       384   |   394       404       414       424      
                            1-MSE                 45-MSE                         76-MSE                                                                                                                        203-MSE                                                               273-MSE                                                                       351|                              388-MSE                                      
                            23                                                                                                                                                                                                                                                                                                                                      355
   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  (2, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

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        TOLB_YERPE | Q8ZGZ1: 4r40

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