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(-) Description

Title :  CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM RHODOBACTER SPHAEROIDES (RSPH17029_3620, TARGET EFI-510199), APO OPEN STRUCTURE
 
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 :  22 Apr 14  (Deposition) - 14 May 14  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym./Biol. Unit :  A
Keywords :  Trap Periplasmic Solute Binding Family, Enzyme Function Initiative, Efi, Structural Genomics (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 DICARBOXYLATE TRANSPORTER-DCTP SUBUNIT
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RSPH17029_3620
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 349101
    Strain: ATCC 17029 / ATH 2.4.9

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 21)

Asymmetric/Biological Unit (5, 21)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3IMD2Ligand/IonIMIDAZOLE
4MSE7Mod. Amino AcidSELENOMETHIONINE
5ZN10Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:212 , PRO A:214 , GLU A:217 , GLN A:298 , LEU A:301 , GLU A:302 , GLU A:305 , ZN A:411binding site for residue IMD A 401
02AC2SOFTWAREGLU A:65 , HIS A:68 , SER A:236 , ASP A:240 , ARG A:299 , GLU A:302 , ZN A:407binding site for residue IMD A 402
03AC3SOFTWARETYR A:252 , PRO A:253 , HIS A:297 , ASP A:300 , HOH A:697 , HOH A:700binding site for residue EDO A 403
04AC4SOFTWAREPRO A:99 , HIS A:110 , PHE A:117 , PHE A:124 , ILE A:157 , LEU A:162 , GLU A:262binding site for residue ACT A 404
05AC5SOFTWAREGLU A:173 , ASP A:231 , TYR A:232 , HOH A:707 , HOH A:710binding site for residue ZN A 405
06AC6SOFTWAREHIS A:49 , HOH A:848 , HOH A:882binding site for residue ZN A 406
07AC7SOFTWAREGLU A:65 , HIS A:68 , ASP A:240 , IMD A:402binding site for residue ZN A 407
08AC8SOFTWAREGLU A:85 , ASP A:245 , GLU A:342 , HOH A:504 , HOH A:586binding site for residue ZN A 408
09AC9SOFTWAREGLU A:196 , HIS A:297 , HOH A:541 , HOH A:612binding site for residue ZN A 409
10AD1SOFTWAREASP A:357 , HOH A:585binding site for residue ZN A 410
11AD2SOFTWAREGLU A:217 , GLU A:305 , IMD A:401 , HOH A:534binding site for residue ZN A 411
12AD3SOFTWAREGLU A:321 , GLU A:322 , HOH A:616binding site for residue ZN A 412
13AD4SOFTWAREASP A:186 , GLU A:363 , HOH A:517 , HOH A:595binding site for residue ZN A 413
14AD5SOFTWAREASP A:317 , HOH A:772 , HOH A:899 , HOH A:900binding site for residue ZN A 414

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PE3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:252 -Pro A:253

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PE3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PE3)

(-) Exons   (0, 0)

(no "Exon" information available for 4PE3)

(-) Sequences/Alignments

Asymmetric/Biological 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:315
                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhhhhhh....eeeee.........hhhhhhhh....eeeee.hhhh..hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......eee.....hhhhhh..eee...hhhhhhhhhh..eee..hhhhhhhhhhh....eee..hhhhhhhhhhhhhh.............eeeeeehhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pe3 A  49 HHFRFQSSDPAGNPNFELQHVFADKVKELTNGEVTIELmPVGTIVDYKETPDAIQAGLIDGHITDTSYFAGRDPAFGLIANPVGAWADPAQmIDFVENGGGKELmNELINPYGLQFIGVSTPGLEAFVSKVPLDTVEDLKGVKVRSPEGLIANVFAAAGANPVNLPSSEVYTSLDKGVIDAADYSVFSVNQDTGmNDIAPHPVYPGFHSLPLVEVSmNKQKWDALTPELQAKITEAQKIFQQTQIDTLHQRDLEAVEAAKAGGKITVHDWSDEERAKFRGIARGEWEKVAGQSEmAQKVYDTLVTYLKDKGLmAE 363
                                    58        68        78        88        98       108       118       128       138 |     148    |  158       168       178       188       198       208       218       228       238    |  248       258      |268       278       288       298       308       318       328       338    |  348       358  |  
                                                                 87-MSE                                              140-MSE      153-MSE                                                                                   243-MSE               265-MSE                                                                       343-MSE           361-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 4PE3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PE3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PE3)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Tyr A:252 - Pro A:253   [ RasMol ]  
 

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