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(-) Description

Title :  CRYSTAL STRUCTURE OF TOLB/PAL COMPLEX FROM YERSINIA PESTIS.
 
Authors :  N. Maltseva, Y. Kim, J. Osipiuk, W. F. Anderson, A. Joachimiak, Center Structural Genomics Of Infectious Diseases (Csgid)
Date :  18 Aug 14  (Deposition) - 03 Sep 14  (Release) - 03 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (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 And Peptidoglycan-Associated Outer Membrane Lipoprotein, 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/Pal Complex From Yersinia Pestis.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROTEIN TOLB
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG68
    Expression System Strain: BL21MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TOLB, Y3055, YPO1124, YP_1032
    Organism Scientific: YERSINIA PESTIS CO92
    Organism Taxid: 214092
    Strain: CO92
 
Molecule 2 - PEPTIDOGLYCAN-ASSOCIATED LIPOPROTEIN
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG68
    Expression System Strain: BL21MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: EXCC, PAL, Y3054, YPO1125, YP_1031
    Organism Scientific: YERSINIA PESTIS CO92
    Organism Taxid: 214092
    Strain: CO92
    Synonym: PEPTIDOGLYCAN-ASSOCIATED LIPOPROTEIN PAL

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 25)

Asymmetric Unit (4, 25)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2GOL3Ligand/IonGLYCEROL
3MSE16Mod. Amino AcidSELENOMETHIONINE
4SO44Ligand/IonSULFATE ION
Biological Unit 1 (4, 14)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2GOL2Ligand/IonGLYCEROL
3MSE8Mod. Amino AcidSELENOMETHIONINE
4SO42Ligand/IonSULFATE ION
Biological Unit 2 (3, 11)
No.NameCountTypeFull Name
1FMT-1Ligand/IonFORMIC ACID
2GOL1Ligand/IonGLYCEROL
3MSE8Mod. Amino AcidSELENOMETHIONINE
4SO42Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:189 , TYR A:190 , ASN A:191 , GLN A:192BINDING SITE FOR RESIDUE SO4 A 501
2AC2SOFTWAREGLY A:286 , ARG A:287 , SER A:288BINDING SITE FOR RESIDUE FMT A 502
3AC3SOFTWAREHIS B:103 , ALA B:104 , GLY B:144 , LYS B:145 , LYS B:147 , PRO B:148 , ASN B:161 , ARG B:163BINDING SITE FOR RESIDUE FMT B 201
4AC4SOFTWAREARG B:91 , LYS B:131 , TRP C:329BINDING SITE FOR RESIDUE GOL B 202
5AC5SOFTWARELYS B:97 , VAL B:98 , ASP B:136 , GLN B:137 , ILE B:138 , SER B:139BINDING SITE FOR RESIDUE GOL B 203
6AC6SOFTWAREARG A:244 , LYS B:125 , ILE B:138 , SER B:139 , ILE B:140BINDING SITE FOR RESIDUE SO4 B 204
7AC7SOFTWAREALA C:56 , ILE C:57 , ALA C:60 , ARG C:142 , TYR C:190BINDING SITE FOR RESIDUE GOL C 501
8AC8SOFTWAREPRO C:77 , GLN C:78 , GLN C:79BINDING SITE FOR RESIDUE SO4 C 502
9AC9SOFTWAREPRO C:243 , SER D:139 , ILE D:140BINDING SITE FOR RESIDUE SO4 D 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R40)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4R40)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R40)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R40)

(-) Exons   (0, 0)

(no "Exon" information available for 4R40)

(-) 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:406
                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....eeeee...ee........hhhhhhhhhhhhh..eee.hhhhh..........hhhhhhh....eeeeeeeee....eeeeeeeeee......eeeeeeeeeee..hhhhhhhhhhhhhhhhhhh.......eeeeeee.......eeeeeee......eeeeee...eeeeee.....eeeeee......eeeeee.....eeeee.....eeeeee.....eeeeee......eeeeee.....eee.......eeeeee.....eeeeee......eeeeee......ee......eeeeeee.....eeeeeeee..eeeeeeee.....eee.......eeeee.....eeeeeeee..eeeeeeee.....eeee...eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r40 A  23 VRIEITQGVDSARPIGVVPFKWmGPGTPPEEIGAIVGADLRNSGKFNPIDAARmPQQPSTAAEVTPAAWTALGIDAVVVGQVQPSADGSYVVSYQLVDTSGSAGSILAQNQYKVTKQWLRYSAHTVSDEVFEKLTGIKGAFRTRIAYVVKTNGGKFPHELRVSDYDGYNQFVVHRSPEPLmSPAWSPDGSKIAYVTFESGKSALVIQTLANGAIRQVASFPRHNGAPAFSPDGTKLAFALSKSGSLNLYVmDLASGQISQVTDGRSNNTEPSWFPDSQNLAYTSDQGGRPQVYKVNINGGVPQRITWEGSQNQNADVSPDGKFLVLVSSNGGAQHIAKQDLETGAVQVLTDTLLDETPSIAPNGTmVIYSSTQGLGSVLQLVSTDGRFKARLPDGQVKFPAWSPYL 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       352       362       372       382     | 392       402       412  ||   424      
                                                 45-MSE                         76-MSE                                                                                                                        203-MSE                                                               273-MSE                                                                                                            388-MSE                    415|            
                                                                                                                                                                                                                                                                                                                                                                                                                                   418            


Chain B from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh.eee.........hhhhhhhhhhhhhhh......eeeee.........hhhhhhhhhhhhhhhhhhhh..hhh.eeeee...........hhhhhhhhheeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r40 B  45 SNLSSEEQARLQmQELQKNNIVYFGFDKYDIGSDFAQmLDAHAAFLRSNPSDKVVVEGHADERGTPEYNIALGERRASAVKmYLQGKGVSADQISIVSYGKEKPAVLGHDEAAFAKNRRAVLVY 168
                                    54  |     64        74       |84        94       104       114       124 |     134       144       154       164    
                                       57-MSE                   82-MSE                                     126-MSE                                      


Chain C from PDB  Type:PROTEIN  Length:405
                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....eeeee...ee........hhhhhhhhhhhh...eee...........hhhhhhhhhhhhh...eeeeeeeee.....eeeeeeeee......eeeeeeeeee...hhhhhhhhhhhhhhhhhhh.......eeeeeee.......eeeeeee......eeeeee....eeeee.....eeeeee......eeeeee.....eeeee.....eeeeee.....eeeeee......eeeeee.....eee.......eeeeee.....eeeeee......eeeeee......ee.......eeeeee.....eeeeeeee..eeeeeeee.....eee.......eeeee.....eeeeeeee..eeeeeeee.....eeee...eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r40 C  23 VRIEITQGVDSARPIGVVPFKWmGPGTPPEEIGAIVGADLRNSGKFNPIDAARmPQQPSTAAEVTPAAWTALGIDAVVVGQVQPSADGSYVVSYQLVDTSGSAGSILAQNQYKVTKQWLRYSAHTVSDEVFEKLTGIKGAFRTRIAYVVKTNGGKFPHELRVSDYDGYNQFVVHRSPEPLmSPAWSPDGSKIAYVTFESGKSALVIQTLANGAIRQVASFPRHNGAPAFSPDGTKLAFALSKSGSLNLYVmDLASGQISQVTDGRSNNTEPSWFPDSQNLAYTSDQGGRPQVYKVNINGGVPQRITWEGSQNQNADVSPDGKFLVLVSSNGGAQHIAKQDLETGAVQVLTDTLLDETPSIAPNGTmVIYSSTQGLGSVLQLVSTDGRFKARLPAGQVKFPAWSPY 429
                                    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       352       362       372       382     | 392       402       412   ||  424     
                                                 45-MSE                         76-MSE                                                                                                                        203-MSE                                                               273-MSE                                                                                                            388-MSE                     416|          
                                                                                                                                                                                                                                                                                                                                                                                                                                    419          


Chain D from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.eee........hhhhh..hhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhhhhhhhhh......eeeeeeehhh......hhhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r40 D  45 SNLSSEEQARLQmQELQKNNIVYFGFDKYDIGSDFAQmLDAHAAFLRSNPSDKVVVEGHADERGTPEYNIALGERRASAVKmYLQGKGVSADQISIVSYGKEKPAVLGHDEAAFAKNRRAVLVY 168
                                    54  |     64        74       |84        94       104       114       124 |     134       144       154       164    
                                       57-MSE                   82-MSE                                     126-MSE
   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 4R40)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R40)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R40)

(-) Gene Ontology  (7, 7)

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  TOLB_YERPE | Q8ZGZ1
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        TOLB_YERPE | Q8ZGZ1: 4pwz
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        Q7CH55_YERPE | Q7CH55: 4pwt

(-) Related Entries Specified in the PDB File

4pwt CRYSTAL STRUCTURE OF PEPTIDOGLYCAN-ASSOCIATED OUTER MEMBRANE LIPOPROTEIN YERSINIA PESTIS RELATED ID: CSGID-IDP00493 RELATED DB: TARGETTRACK RELATED ID: CSGID-IDP00403 RELATED DB: TARGETTRACK
4pwz CRYSTAL STRUCTURE OF TOLB PROTEIN FROM YERSINIA PESTIS