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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE MANDELATE RACEMASE FROM BORDETELLA BRONCHISEPTICA RB50
 
Authors :  V. N. Malashkevich, R. Toro, C. Morano, J. M. Sauder, S. K. Burley, S. C. A York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  10 Apr 09  (Deposition) - 21 Apr 09  (Release) - 24 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Keywords :  Structural Genomics, Crystal Structure, Protein Structure Initiative, New York Structural Genomix Research Consortium, Nysgxrc, Enolase, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. N. Malashkevich, R. Toro, C. Morano, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Putative Mandelate Racemase From Bordetella Bronchiseptica Rb50
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 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: 562
    Expression System Vector Type: PLASMID
    Gene: BB4687
    Organism Common: ALCALIGENES BRONCHISEPTICUS
    Organism Scientific: BORDETELLA BRONCHISEPTICA
    Organism Taxid: 518
    Strain: RB50

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (4x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:201 , GLU A:227 , GLU A:254 , HOH A:475 , HOH A:534 , HOH A:594BINDING SITE FOR RESIDUE NA A 500
2AC2SOFTWAREASP B:201 , GLU B:227 , GLU B:254 , HOH B:432 , HOH B:540 , HOH B:579BINDING SITE FOR RESIDUE NA B 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H12)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric 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 3H12)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3H12)

(-) Exons   (0, 0)

(no "Exon" information available for 3H12)

(-) 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:392
 aligned with A0A0H3LT39_B | A0A0H3LT39 from UniProtKB/TrEMBL  Length:387

    Alignment length:392
                             1                                                                                                                                                                                                                                                                                                                                                                                               387    
                             |       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     - -MKITEVKAHALSTPIPERMRVESGAGLKLNRQMILVEVRTDEGVTGVGSPSGPYDLAVLKRAIEDVIGPQLIGEDPANINYLWHKVFHGEVSRNLGHRSVGIAAMSGVDIALWDLKGRAMNQPIYQLLGGKFHTRGVRAYASSIYWDLTPDQAADELAGWVEQGFTAAKLKVGRAPRKDAANLRAMRQRVGADVEILVDANQSLGRHDALAMLRILDEAGCYWFEEPLSIDDIEGHRILRAQGTPVRIATGENLYTRNAFNDYIRNDAIDVLQADASRAGGITEALAISASAASAHLAWNPHTFNDIITVAANLHLVAASPHPAMFEWDITHNDLMTRLASYDLKLENGLVQPPQGPGLGFEIDWDFVAAHAWKGEPAIGAGHGMKK----   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeee.hhhhh.ee..ee..eeeeeeeeeee.....eee......hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh........eeeeeeee....hhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh...eee......hhhhhhhhhh.....eeee....hhhhhhhhhhhh....ee........hhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhh.....eeee...hhhhh............ee............hhhhhhhh............hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h12 A   2 SLKITEVKAHALSTPIPERMRVESGAGLKLNRQMILVEVRTDEGVTGVGSPSGPYDLAVLKRAIEDVIGPQLIGEDPANINYLWHKVFHGEVSRNLGHRSVGIAAMSGVDIALWDLKGRAMNQPIYQLLGGKFHTRGVRAYASSIYWDLTPDQAADELAGWVEQGFTAAKLKVGRAPRKDAANLRAMRQRVGADVEILVDANQSLGRHDALAMLRILDEAGCYWFEEPLSIDDIEGHRILRAQGTPVRIATGENLYTRNAFNDYIRNDAIDVLQADASRAGGITEALAISASAASAHLAWNPHTFNDIITVAANLHLVAASPHPAMFEWDITHNDLMTRLASYDLKLENGLVQPPQGPGLGFEIDWDFVAAHAWKGEPAIGAGHGMKKEGHH 393
                                    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       391  


Chain B from PDB  Type:PROTEIN  Length:392
 aligned with A0A0H3LT39_B | A0A0H3LT39 from UniProtKB/TrEMBL  Length:387

    Alignment length:392
                             1                                                                                                                                                                                                                                                                                                                                                                                               387    
                             |       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     - -MKITEVKAHALSTPIPERMRVESGAGLKLNRQMILVEVRTDEGVTGVGSPSGPYDLAVLKRAIEDVIGPQLIGEDPANINYLWHKVFHGEVSRNLGHRSVGIAAMSGVDIALWDLKGRAMNQPIYQLLGGKFHTRGVRAYASSIYWDLTPDQAADELAGWVEQGFTAAKLKVGRAPRKDAANLRAMRQRVGADVEILVDANQSLGRHDALAMLRILDEAGCYWFEEPLSIDDIEGHRILRAQGTPVRIATGENLYTRNAFNDYIRNDAIDVLQADASRAGGITEALAISASAASAHLAWNPHTFNDIITVAANLHLVAASPHPAMFEWDITHNDLMTRLASYDLKLENGLVQPPQGPGLGFEIDWDFVAAHAWKGEPAIGAGHGMKK----   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeee.hhhhh.ee..ee..eeeeeeeeeee.....eee......hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh........eeeeeeee....hhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh...eee......hhhhhhhhhh.....eeee....hhhhhhhhhhhh....ee........hhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhh.....eeee...hhhhh............ee............hhhhhhhh............hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h12 B   2 SLKITEVKAHALSTPIPERMRVESGAGLKLNRQMILVEVRTDEGVTGVGSPSGPYDLAVLKRAIEDVIGPQLIGEDPANINYLWHKVFHGEVSRNLGHRSVGIAAMSGVDIALWDLKGRAMNQPIYQLLGGKFHTRGVRAYASSIYWDLTPDQAADELAGWVEQGFTAAKLKVGRAPRKDAANLRAMRQRVGADVEILVDANQSLGRHDALAMLRILDEAGCYWFEEPLSIDDIEGHRILRAQGTPVRIATGENLYTRNAFNDYIRNDAIDVLQADASRAGGITEALAISASAASAHLAWNPHTFNDIITVAANLHLVAASPHPAMFEWDITHNDLMTRLASYDLKLENGLVQPPQGPGLGFEIDWDFVAAHAWKGEPAIGAGHGMKKEGHH 393
                                    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       391
   Legend:   → Mismatch (orange background)
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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 3H12)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3H12)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H12)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3H12)

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        A0A0H3LT39_B | A0A0H3LT39: 3op2 3ozm 3ozy

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