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(-) Description

Title :  CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM SULFITOBACTER SP. NAS-14.1 (TARGET EFI-510299) WITH BOUND BETA-D-GALACTURONATE
 
Authors :  M. W. Vetting, N. F. Al Obaidi, L. L. Morisco, S. R. Wasserman, M. Stead, J. D. Attonito, A. Scott Glenn, S. Chowdhury, B. Evans, B. Hillerich, R. D. Seidel, K. L. Whalen, J. A. Gerlt, S. C. Almo, Enzyme Function In (Efi)
Date :  28 Apr 14  (Deposition) - 14 May 14  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Trap Periplasmic Solute Binding Family, Enzyme Function Initiative, Efi, Structural Genomics, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. W. Vetting, N. Al-Obaidi, S. Zhao, B. San Francisco, J. Kim, D. J. Wichelecki, J. T. Bouvier, J. O. Solbiati, H. Vu, X. Zhang, D. A. Rodionov, J. D. Love, B. S. Hillerich, R. D. Seidel, R. J. Quinn, A. L. Osterman, J. E. Cronan, M. P. Jacobson, J. A. Gerlt, S. C. Almo
Experimental Strategies For Functional Annotation And Metabolism Discovery: Targeted Screening Of Solute Binding Proteins And Unbiased Panning Of Metabolomes.
Biochemistry V. 54 909 2015
PubMed-ID: 25540822  |  Reference-DOI: 10.1021/BI501388Y

(-) Compounds

Molecule 1 - TRAP-T FAMILY TRANSPORTER, DCTP (PERIPLASMIC BINDING) SUBUNIT
    Chains: A, B
    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 30-331
    Gene: NAS141_03681
    Organism Scientific: SULFITOBACTER SP. NAS-14.1
    Organism Taxid: 314267

 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  (3, 36)

Asymmetric Unit (3, 36)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GTR2Ligand/IonBETA-D-GALACTOPYRANURONIC ACID
3MSE32Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 17)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GTR1Ligand/IonBETA-D-GALACTOPYRANURONIC ACID
3MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 17)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GTR1Ligand/IonBETA-D-GALACTOPYRANURONIC ACID
3MSE16Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:71 , ALA A:190 , PHE A:191 , HOH A:595 , HOH A:691binding site for residue CL A 401
2AC2SOFTWAREILE A:32 , HIS A:33 , GLN A:71 , SER A:89 , ARG A:147 , ARG A:168 , MSE A:170 , PHE A:191 , ASN A:208 , ASN A:209 , SER A:212 , GLU A:235 , HOH A:574 , HOH A:576 , HOH A:581 , HOH A:583binding site for residue GTR A 402
3AC3SOFTWAREGLN B:71 , ALA B:190 , PHE B:191 , HOH B:603binding site for residue CL B 401
4AC4SOFTWAREILE B:32 , HIS B:33 , GLN B:71 , SER B:89 , ARG B:147 , ARG B:168 , MSE B:170 , PHE B:191 , ASN B:208 , ASN B:209 , SER B:212 , GLU B:235 , HOH B:574 , HOH B:577 , HOH B:578 , HOH B:581binding site for residue GTR B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PF8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4PF8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PF8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PF8)

(-) Exons   (0, 0)

(no "Exon" information available for 4PF8)

(-) 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:300
                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee......hhhhhhhhhhhhhhhhhh.....eeee......hhhhhhhhhhh....eeeeehhhhh..hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....eeeee......hhhhhh..eeee..hhhhhhhhhh...eeee.hhhhhhhhhhh....eeeehhhhhhhhhhhhhh.eeeeeeee...eeeeeehhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4pf8 A  26 DWRGWNIHVEDYPVSHGmEAFmEEVTEKTGGEIKGKVFHAGVLGSQPDAIEQLRLGImDFGVFSLGPmGQAVPATNVVSLPFVFKSVPQmYELmDGEPGAALGKALEEKGIVALGYYDAGARSFYNSVKPINTPEDVQGmKVRVmNNDLFVGmIESmGGNATPmAFAEVYQSIKTGVVDGAENNPPSYESTSHFEVAKYYSLTQHLIIPECLCmSKKTFDGLTPEQQEIVKTAGKNSTDLQRKLWGEREAASmKIImDGGVEVNEIADKSAFQEAmVPVYEKYLAANPEmTDLVNLFRNA 325
                                    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
                                            43-MSE                                  83-MSE    93-MSE               115-MSE                                           165-MSE|     178-MSE      |                                               239-MSE                                278-MSE                301-MSE       315-MSE      
                                                47-MSE                                                                 119-MSE                                            170-MSE     182-MSE  |                                                                                          282-MSE                                       
                                                                                                                                                                                             189-MSE                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:300
                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhh....eeeeehhhhh..hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....eeeee......hhhhhh..eeee..hhhhhhhhhh...eeee.hhhhhhhhhhh....eeeehhhhhhhhhhhhhh.eeeeeeee...eeeeeehhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4pf8 B  25 KDWRGWNIHVEDYPVSHGmEAFmEEVTEKTGGEIKGKVFHAGVLGSQPDAIEQLRLGImDFGVFSLGPmGQAVPATNVVSLPFVFKSVPQmYELmDGEPGAALGKALEEKGIVALGYYDAGARSFYNSVKPINTPEDVQGmKVRVmNNDLFVGmIESmGGNATPmAFAEVYQSIKTGVVDGAENNPPSYESTSHFEVAKYYSLTQHLIIPECLCmSKKTFDGLTPEQQEIVKTAGKNSTDLQRKLWGEREAASmKIImDGGVEVNEIDKSAFQEAmVPVYEKYLAANPEmTDLVNLFRNA 325
                                    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      |295     | 305       315       325
                                             43-MSE                                  83-MSE    93-MSE               115-MSE                                           165-MSE|     178-MSE      |                                               239-MSE                                278-MSE      291|     301-MSE       315-MSE      
                                                 47-MSE                                                                 119-MSE                                            170-MSE     182-MSE  |                                                                                          282-MSE   293                                
                                                                                                                                                                                              189-MSE
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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  (0, 0)

(no "SCOP Domain" information available for 4PF8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PF8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PF8)

(-) Gene Ontology  (2, 2)

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4pf6