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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE MANDELATE RACEMASE FROM BORDETELLA BRONCHISEPTICA RB50 COMPLEXED WITH 2-OXOGLUTARATE/PHOSPHATE
 
Authors :  V. N. Malashkevich, Y. Patskovsky, U. Ramagopal, R. Toro, J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center For Struct Genomics (Nysgxrc)
Date :  31 Aug 10  (Deposition) - 15 Sep 10  (Release) - 15 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Protein Structure Initiative, New York Structural Genomix Research Consortium, Nysgxrc, Racemase, 2- Oxoglutarate, Psi-2, New York Sgx Research Center For Structural Genomics, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. N. Malashkevich, Y. Patskovsky, U. Ramagopal, R. Toro, J. M. Sauder S. K. Burley, S. C. Almo
Crystal Structure Of Putative Mandelate Racemase From Bordetella Bronchiseptica Rb50 Complexed With 2-Oxoglutarate/Phosphate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE MANDELATE RACEMASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)CODON+RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BB4687
    Organism Scientific: BORDETELLA BRONCHISEPTICA
    Organism Taxid: 518
    Strain: RB50

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 20)

Asymmetric/Biological Unit (4, 20)
No.NameCountTypeFull Name
1AKG1Ligand/Ion2-OXOGLUTARIC ACID
2MG2Ligand/IonMAGNESIUM ION
3MSE16Mod. Amino AcidSELENOMETHIONINE
4PO41Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:201 , GLU A:227 , GLU A:254 , AKG A:501 , HOH A:736BINDING SITE FOR RESIDUE MG A 500
2AC2SOFTWARELYS A:171 , LYS A:173 , ASP A:201 , ASN A:203 , GLU A:227 , GLU A:254 , HIS A:304 , PHE A:306 , GLU A:329 , MG A:500BINDING SITE FOR RESIDUE AKG A 501
3AC3SOFTWARELYS B:173 , ASP B:201 , GLU B:227 , GLU B:254 , PO4 B:501 , HOH B:634 , HOH B:781BINDING SITE FOR RESIDUE MG B 500
4AC4SOFTWARESER B:144 , SER B:145 , LYS B:171 , LYS B:173 , ASP B:201 , GLU B:227 , GLU B:254 , HIS B:304 , PHE B:306 , GLU B:329 , MG B:500 , HOH B:602 , HOH B:781 , HOH B:863BINDING SITE FOR RESIDUE PO4 B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OP2)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:54 -Pro A:55
2Ser A:144 -Ser A:145
3Gly B:54 -Pro B:55
4Ser B:144 -Ser B:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OP2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OP2)

(-) Exons   (0, 0)

(no "Exon" information available for 3OP2)

(-) 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:375
 aligned with A0A0H3LT39_B | A0A0H3LT39 from UniProtKB/TrEMBL  Length:387

    Alignment length:380
                             1                                                                                                                                                                                                                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379
         A0A0H3LT39_B     - -MKITEVKAHALSTPIPERMRVESGAGLKLNRQMILVEVRTDEGVTGVGSPSGPYDLAVLKRAIEDVIGPQLIGEDPANINYLWHKVFHGEVSRNLGHRSVGIAAMSGVDIALWDLKGRAMNQPIYQLLGGKFHTRGVRAYASSIYWDLTPDQAADELAGWVEQGFTAAKLKVGRAPRKDAANLRAMRQRVGADVEILVDANQSLGRHDALAMLRILDEAGCYWFEEPLSIDDIEGHRILRAQGTPVRIATGENLYTRNAFNDYIRNDAIDVLQADASRAGGITEALAISASAASAHLAWNPHTFNDIITVAANLHLVAASPHPAMFEWDITHNDLMTRLASYDLKLENGLVQPPQGPGLGFEIDWDFVAAHAWKGEPAI 379
               SCOP domains d3op2a1 A:2-132 automated matches                                                                                                  d3op2a2 A:133-381 automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeee...............eeeeeeeeeee.....eee......hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh...-----hhhhhhhhhhhhhhhhhhhhhh..hhhhhh........eeeeeeee....hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh...eee......hhhhhhhhhhh....eeee.....hhhhhhhhhhh....ee.......hhhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhh.....eeee...hhhhhh...........ee............hhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3op2 A   2 SLKITEVKAHALSTPIPERmRVESGAGLKLNRQmILVEVRTDEGVTGVGSPSGPYDLAVLKRAIEDVIGPQLIGEDPANINYLWHKVFHGEVSR-----SVGIAAmSGVDIALWDLKGRAmNQPIYQLLGGKFHTRGVRAYASSIYWDLTPDQAADELAGWVEQGFTAAKLKVGRAPRKDAANLRAmRQRVGADVEILVDANQSLGRHDALAmLRILDEAGCYWFEEPLSIDDIEGHRILRAQGTPVRIATGENLYTRNAFNDYIRNDAIDVLQADASRAGGITEALAISASAASAHLAWNPHTFNDIITVAANLHLVAASPHPAmFEWDITHNDLmTRLASYDLKLENGLVQPPQGPGLGFEIDWDFVAAHAWKGEPAI 381
                                    11        21        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       361       371       381
                                              21-MSE        35-MSE                                                      95   101     |            122-MSE                                                           188-MSE                   214-MSE                                                                                                          327-MSE    338-MSE                                       
                                                                                                                                   107-MSE                                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:368
 aligned with A0A0H3LT39_B | A0A0H3LT39 from UniProtKB/TrEMBL  Length:387

    Alignment length:379
                             1                                                                                                                                                                                                                                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369         
         A0A0H3LT39_B     - -MKITEVKAHALSTPIPERMRVESGAGLKLNRQMILVEVRTDEGVTGVGSPSGPYDLAVLKRAIEDVIGPQLIGEDPANINYLWHKVFHGEVSRNLGHRSVGIAAMSGVDIALWDLKGRAMNQPIYQLLGGKFHTRGVRAYASSIYWDLTPDQAADELAGWVEQGFTAAKLKVGRAPRKDAANLRAMRQRVGADVEILVDANQSLGRHDALAMLRILDEAGCYWFEEPLSIDDIEGHRILRAQGTPVRIATGENLYTRNAFNDYIRNDAIDVLQADASRAGGITEALAISASAASAHLAWNPHTFNDIITVAANLHLVAASPHPAMFEWDITHNDLMTRLASYDLKLENGLVQPPQGPGLGFEIDWDFVAAHAWKGEPA 378
               SCOP domains d3op2b1 B:2-132 automa      ted matches                                                                                            d3op2b2 B:133-380 automated matches                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeee.......------..eeeeeeeeeee.....eee......hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.....-----hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh........eeeeeeee....hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhh....eeee.....hhhhhhhhhhh....ee.......hhhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhh.....eeee...hhhhhh...........ee............hhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3op2 B   2 SLKITEVKAHALSTPIPERmRV------KLNRQmILVEVRTDEGVTGVGSPSGPYDLAVLKRAIEDVIGPQLIGEDPANINYLWHKVFHGEVSR-----SVGIAAmSGVDIALWDLKGRAmNQPIYQLLGGKFHTRGVRAYASSIYWDLTPDQAADELAGWVEQGFTAAKLKVGRAPRKDAANLRAmRQRVGADVEILVDANQSLGRHDALAmLRILDEAGCYWFEEPLSIDDIEGHRILRAQGTPVRIATGENLYTRNAFNDYIRNDAIDVLQADASRAGGITEALAISASAASAHLAWNPHTFNDIITVAANLHLVAASPHPAmFEWDITHNDLmTRLASYDLKLENGLVQPPQGPGLGFEIDWDFVAAHAWKGEPA 380
                                    11        21 |      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       361       371         
                                              21-MSE   30    |                                                          95   101     |            122-MSE                                                           188-MSE                   214-MSE                                                                                                          327-MSE    338-MSE                                      
                                                23          35-MSE                                                                 107-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OP2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3OP2)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3OP2)

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  Cis Peptide Bonds
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    Ser B:144 - Ser B:145   [ RasMol ]  
 

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 Related Entries

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UniProtKB/TrEMBL
        A0A0H3LT39_B | A0A0H3LT39: 3h12 3ozm 3ozy

(-) Related Entries Specified in the PDB File

3h12 RELATED ID: NYSGXRC-9280A RELATED DB: TARGETDB