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(-) Description

Title :  CRYSTAL STRUCTURE OF A SHORT CHAIN DEHYDROGENASE FROM AGROBACTERIUM TUMEFACIENS
 
Authors :  J. B. Bonanno, M. Rutter, K. T. Bain, S. Chang, R. Romero, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center Structural Genomics (Nysgxrc)
Date :  03 Sep 08  (Deposition) - 30 Sep 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Dehydrogenase, Oxidoreductase, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Bonanno, M. Rutter, K. T. Bain, S. Chang, R. Romero, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of A Short Chain Dehydrogenase From Agrobacterium Tumefaciens
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SHORT CHAIN DEHYDROGENASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET26
    Expression System Strain: BL21(DE3)
    Expression System Vector Type: PLASMID
    Gene: AGR_L_3556, ATU3026
    Organism Scientific: AGROBACTERIUM TUMEFACIENS STR.
    Organism Taxid: 176299
    Strain: C58

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3EDM)

(-) Sites  (0, 0)

(no "Site" information available for 3EDM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:175 -Pro A:176
2Gly B:175 -Pro B:176
3Gly C:175 -Pro C:176
4Gly D:175 -Pro D:176

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3EDM)

(-) 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:226
 aligned with A9CEK0_AGRFC | A9CEK0 from UniProtKB/TrEMBL  Length:249

    Alignment length:248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241        
         A9CEK0_AGRFC     2 QRFTNRTIVVAGAGRDIGRACAIRFAQEGANVVLTYNGAAEGAATAVAEIEKLGRSALAIKADLTNAAEVEAAISAAADKFGEIHGLVHVAGGLIARKTIAEMDEAFWHQVLDVNLTSLFLTAKTALPKMAKGGAIVTFSSQAGRDGGGPGALAYATSKGAVMTFTRGLAKEVGPKIRVNAVCPGMISTTFHDTFTKPEVRERVAGATSLKREGSSEDVAGLVAFLASDDAAYVTGACYDINGGVLFS 249
               SCOP domains d3edma_ A: automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhh.eeeeee..............hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....----------------------...hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3edm A   2 QRFTNRTIVVAGAGRDIGRACAIRFAQEGANVVLTYNGAAEGAATAVAEIEKLGRSALAIKADLTNAAEVEAAISAAADKFGEIHGLVHVAGGLIARKTIAEMDEAFWHQVLDVNLTSLFLTAKTALPKMAKGGAIVTFSSQAGRDGGGPGALAYATSKGAVMTFTRGLAKEVGPKIRVNAVCPGMIST----------------------REGSSEDVAGLVAFLASDDAAYVTGACYDINGGVLFS 249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181        |-         -         - |     221       231       241        
                                                                                                                                                                                                                      190                    213                                    


Chain B from PDB  Type:PROTEIN  Length:227
 aligned with A9CEK0_AGRFC | A9CEK0 from UniProtKB/TrEMBL  Length:249

    Alignment length:248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241        
         A9CEK0_AGRFC     2 QRFTNRTIVVAGAGRDIGRACAIRFAQEGANVVLTYNGAAEGAATAVAEIEKLGRSALAIKADLTNAAEVEAAISAAADKFGEIHGLVHVAGGLIARKTIAEMDEAFWHQVLDVNLTSLFLTAKTALPKMAKGGAIVTFSSQAGRDGGGPGALAYATSKGAVMTFTRGLAKEVGPKIRVNAVCPGMISTTFHDTFTKPEVRERVAGATSLKREGSSEDVAGLVAFLASDDAAYVTGACYDINGGVLFS 249
               SCOP domains d3edmb_ B: automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhh.eeeeee..............hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee...---------------------...hhhhhhhhhhhhhhhhhh.....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3edm B   2 QRFTNRTIVVAGAGRDIGRACAIRFAQEGANVVLTYNGAAEGAATAVAEIEKLGRSALAIKADLTNAAEVEAAISAAADKFGEIHGLVHVAGGLIARKTIAEMDEAFWHQVLDVNLTSLFLTAKTALPKMAKGGAIVTFSSQAGRDGGGPGALAYATSKGAVMTFTRGLAKEVGPKIRVNAVCPGMISTT---------------------REGSSEDVAGLVAFLASDDAAYVTGACYDINGGVLFS 249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191         -         - |     221       231       241        
                                                                                                                                                                                                                       191                   213                                    


Chain C from PDB  Type:PROTEIN  Length:214
 aligned with A9CEK0_AGRFC | A9CEK0 from UniProtKB/TrEMBL  Length:249

    Alignment length:243
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241   
         A9CEK0_AGRFC     2 QRFTNRTIVVAGAGRDIGRACAIRFAQEGANVVLTYNGAAEGAATAVAEIEKLGRSALAIKADLTNAAEVEAAISAAADKFGEIHGLVHVAGGLIARKTIAEMDEAFWHQVLDVNLTSLFLTAKTALPKMAKGGAIVTFSSQAGRDGGGPGALAYATSKGAVMTFTRGLAKEVGPKIRVNAVCPGMISTTFHDTFTKPEVRERVAGATSLKREGSSEDVAGLVAFLASDDAAYVTGACYDING 244
               SCOP domains d3edmc_ C: automated matches                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh.eeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeee.-----------------------------.hhhhhhhhhhhhhhhhhh.....eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3edm C   2 QRFTNRTIVVAGAGRDIGRACAIRFAQEGANVVLTYNGAAEGAATAVAEIEKLGRSALAIKADLTNAAEVEAAISAAADKFGEIHGLVHVAGGLIARKTIAEMDEAFWHQVLDVNLTSLFLTAKTALPKMAKGGAIVTFSSQAGRDGGGPGALAYATSKGAVMTFTRGLAKEVGPKIRVNAVCP-----------------------------GSSEDVAGLVAFLASDDAAYVTGACYDING 244
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181   |     -         -         -   |   221       231       241   
                                                                                                                                                                                                                 185                           215                             


Chain D from PDB  Type:PROTEIN  Length:213
 aligned with A9CEK0_AGRFC | A9CEK0 from UniProtKB/TrEMBL  Length:249

    Alignment length:243
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241   
         A9CEK0_AGRFC     2 QRFTNRTIVVAGAGRDIGRACAIRFAQEGANVVLTYNGAAEGAATAVAEIEKLGRSALAIKADLTNAAEVEAAISAAADKFGEIHGLVHVAGGLIARKTIAEMDEAFWHQVLDVNLTSLFLTAKTALPKMAKGGAIVTFSSQAGRDGGGPGALAYATSKGAVMTFTRGLAKEVGPKIRVNAVCPGMISTTFHDTFTKPEVRERVAGATSLKREGSSEDVAGLVAFLASDDAAYVTGACYDING 244
               SCOP domains d3edmd_ D: automated matches                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee..-hhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh.eeeeee..............hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeee.-----------------------------.hhhhhhhhhhhhhhhhhh.....eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3edm D   2 QRFTNRTIVVAGAGRDIGRACAIRFAQEGANVVLTYNG-AEGAATAVAEIEKLGRSALAIKADLTNAAEVEAAISAAADKFGEIHGLVHVAGGLIARKTIAEMDEAFWHQVLDVNLTSLFLTAKTALPKMAKGGAIVTFSSQAGRDGGGPGALAYATSKGAVMTFTRGLAKEVGPKIRVNAVCP-----------------------------GSSEDVAGLVAFLASDDAAYVTGACYDING 244
                                    11        21        31       |41        51        61        71        81        91       101       111       121       131       141       151       161       171       181   |     -         -         -   |   221       231       241   
                                                                39 |                                                                                                                                             185                           215                             
                                                                  41
   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  (1, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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  Cis Peptide Bonds
    Gly A:175 - Pro A:176   [ RasMol ]  
    Gly B:175 - Pro B:176   [ RasMol ]  
    Gly C:175 - Pro C:176   [ RasMol ]  
    Gly D:175 - Pro D:176   [ RasMol ]  
 

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