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(-) Description

Title :  CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS (DEVAL_0042, TARGET EFI-510114) BOUND TO COPURIFIED (R)-PANTOIC ACID
 
Authors :  M. W. Vetting, N. F. Al Obaidi, R. Toro, L. L. Morisco, J. Benach, S. R. Wa J. D. Attonito, A. Scott Glenn, S. Chamala, S. Chowdhury, J. Lafleur, R. D. Seidel, K. L. Whalen, J. A. Gerlt, S. C. Almo, Enzyme Function In (Efi)
Date :  24 Dec 14  (Deposition) - 28 Jan 15  (Release) - 28 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Trap Periplasmic Solute Binding Family, Enzyme Function Initiative, Efi, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. W. Vetting, N. F. Al Obaidi, R. Toro, L. L. Morisco, J. Benach, S. R. Wasserman, J. D. Attonito, A. Scott Glenn, S. Chamala, S. Chowdhury, J. Lafleur, J. Love, R. D. Seidel, K. L. Whalen, J. A. Gerlt, S. C. Almo, Enzyme Function Initiative (Efi)
Crystal Structure Of A Trap Periplasmic Solute Binding Protein From Desulfovibrio Vulgaris (Deval_0042, Target Efi-510114) Bound To Copurified (R)-Pantoic Acid
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRAP DICARBOXYLATE TRANSPORTER, DCTP SUBUNIT
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 37-341
    Gene: DEVAL_0042
    Organism Scientific: DESULFOVIBRIO VULGARIS
    Organism Taxid: 573059
    Strain: RCH1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 36)

Asymmetric Unit (2, 36)
No.NameCountTypeFull Name
1MSE32Mod. Amino AcidSELENOMETHIONINE
2PAF4Ligand/IonPANTOATE
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2PAF1Ligand/IonPANTOATE
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2PAF1Ligand/IonPANTOATE
Biological Unit 3 (2, 9)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2PAF1Ligand/IonPANTOATE
Biological Unit 4 (2, 9)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2PAF1Ligand/IonPANTOATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:45 , GLN A:52 , THR A:102 , ASN A:157 , ARG A:160 , ARG A:181 , MSE A:183 , TRP A:204 , ASN A:220 , HIS A:247 , HOH A:566binding site for residue PAF A 401
2AC2SOFTWAREGLN B:52 , THR B:102 , ASN B:157 , ARG B:160 , ARG B:181 , MSE B:183 , TRP B:204 , ASN B:220 , HIS B:247 , HOH B:551binding site for residue PAF B 401
3AC3SOFTWAREGLN C:52 , THR C:102 , ASN C:157 , ARG C:160 , ARG C:181 , MSE C:183 , TRP C:204 , ASN C:220 , HIS C:247 , HOH C:522binding site for residue PAF C 401
4AC4SOFTWAREGLN D:52 , THR D:102 , ASN D:157 , ARG D:160 , ARG D:181 , MSE D:183 , TRP D:204 , ASN D:220 , HIS D:247 , HOH D:537binding site for residue PAF D 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Trp A:204 -Pro A:205
2Trp B:204 -Pro B:205
3Trp C:204 -Pro C:205
4Trp D:204 -Pro D:205

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XEQ)

(-) 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:303
                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee.eeee......hhhhhh....ee..hhhhhhhhhhh....ee....hhhhhhh....eeeehhhhhhhhhhhhh..eee.....eeeeeeeeehhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xeq A  37 AEDITLAVVTKPGSAQYVCAERFAQLLAERSDKRFNVVLHHSASLGTETDILQQVQLGAVQmAIVTTGTLDAFVPEmAALDFPFLFTDTTTADRVLDGPVGRGLLDRLSTAGFKGLHFSENGFRHLTNSIRPVmTPDDVRGLKIRVmESQVHRELWRTLGANPTPmGWPIYAELQQGTLDGQENPLWVIAEYRLNEVQKHLSLTGHVYSTHTDLANLAWFEALPANDRRLLASCmQDAALWQRTWSRQRDAAYLEQLRTAGmQVIERPDIATFRQRVQPLSGSALFEHKGVRKALEDLmAATR 339
                                    46        56        66        76        86        96 |     106      |116       126       136       146       156       166   |   176      |186       196     | 206       216       226       236       246       256       266    |  276       286       296 |     306       316       326       336   
                                                                                        98-MSE        113-MSE                                                  170-MSE      183-MSE            202-MSE                                                              271-MSE                    298-MSE                              335-MSE


Chain B from PDB  Type:PROTEIN  Length:304
                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......hhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeeee......hhhhhh....ee..hhhhhhhhhhh....ee....hhhhhhh....eeeehhhhhhhhhhhhhh.eeeeeeeeeeeeeeeeehhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xeq B  37 AEDITLAVVTKPGSAQYVCAERFAQLLAERSDKRFNVVLHHSASLGTETDILQQVQLGAVQmAIVTTGTLDAFVPEmAALDFPFLFTDTTTADRVLDGPVGRGLLDRLSTAGFKGLHFSENGFRHLTNSIRPVmTPDDVRGLKIRVmESQVHRELWRTLGANPTPmGWPIYAELQQGTLDGQENPLWVIAEYRLNEVQKHLSLTGHVYSTHTDLANLAWFEALPANDRRLLASCmQDAALWQRTWSRQRDAAYLEQLRTAGmQVIERPDIATFRQRVQPLSGSALFEHKGVRKALEDLmAATRA 340
                                    46        56        66        76        86        96 |     106      |116       126       136       146       156       166   |   176      |186       196     | 206       216       226       236       246       256       266    |  276       286       296 |     306       316       326       336    
                                                                                        98-MSE        113-MSE                                                  170-MSE      183-MSE            202-MSE                                                              271-MSE                    298-MSE                              335-MSE 


Chain C from PDB  Type:PROTEIN  Length:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeeee................ee..hhhhhhhhhhhh...ee....hhhhhhh....eeeehhhhhhhhhhhhhh.eeeeeeeeeeeeeeeeehhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xeq C  38 EDITLAVVTKPGSAQYVCAERFAQLLAERSDKRFNVVLHHSASLGTETDILQQVQLGAVQmAIVTTGTLDAFVPEmAALDFPFLFTDTTTADRVLDGPVGRGLLDRLSTAGFKGLHFSENGFRHLTNSIRPVmTPDDVRGLKIRVmESQVHRELWRTLGANPTPmGWPIYAELQQGTLDGQENPLWVIAEYRLNEVQKHLSLTGHVYSTHTDLANLAWFEALPANDRRLLASCmQDAALWQRTWSRQRDAAYLEQLRTAGmQVIERPDIATFRQRVQPLSGSALFEHKGVRKALEDLmAATR 339
                                    47        57        67        77        87        97|      107     | 117       127       137       147       157       167  |    177     | 187       197    |  207       217       227       237       247       257       267   |   277       287       297|      307       317       327       337  
                                                                                       98-MSE        113-MSE                                                  170-MSE      183-MSE            202-MSE                                                              271-MSE                    298-MSE                              335-MSE


Chain D from PDB  Type:PROTEIN  Length:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhh....eeeee.hhhh..hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee.eeee......hhhhhh....ee..hhhhhhhhhhh....ee....hhhhhhh....eeeehhhhhhhhhhhhh..eee.....eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xeq D  38 EDITLAVVTKPGSAQYVCAERFAQLLAERSDKRFNVVLHHSASLGTETDILQQVQLGAVQmAIVTTGTLDAFVPEmAALDFPFLFTDTTTADRVLDGPVGRGLLDRLSTAGFKGLHFSENGFRHLTNSIRPVmTPDDVRGLKIRVmESQVHRELWRTLGANPTPmGWPIYAELQQGTLDGQENPLWVIAEYRLNEVQKHLSLTGHVYSTHTDLANLAWFEALPANDRRLLASCmQDAALWQRTWSRQRDAAYLEQLRTAGmQVIERPDIATFRQRVQPLSGSALFEHKGVRKALEDLmAATR 339
                                    47        57        67        77        87        97|      107     | 117       127       137       147       157       167  |    177     | 187       197    |  207       217       227       237       247       257       267   |   277       287       297|      307       317       327       337  
                                                                                       98-MSE        113-MSE                                                  170-MSE      183-MSE            202-MSE                                                              271-MSE                    298-MSE                              335-MSE
   Legend:   → Mismatch (orange background)
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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 4XEQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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4xf5 4xfe