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(-) Description

Title :  ENSEMBLE REFINEMENT OF THE PROTEIN CRYSTAL STRUCTURE OF PUTATIVE TROPINONE REDUCTASE FROM ARABIDOPSIS THALIANA GENE AT1G07440
 
Authors :  E. J. Levin, D. A. Kondrashov, G. E. Wesenberg, G. N. Phillips Jr. , Cent Eukaryotic Structural Genomics (Cesg)
Date :  31 May 07  (Deposition) - 19 Jun 07  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A  (8x)
Biol. Unit 1:  A  (4x)
Keywords :  Ensemble Refinement, Refinement Methodology Development, At1G07440, Reductively Methylated Protein, Putative Tropinone Reductase, Structural Genomics, Protein Structure Initiative, Psi, Center For Eukaryotic Structural Genomics, Cesg, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. J. Levin, D. A. Kondrashov, G. E. Wesenberg, G. N. Phillips
Ensemble Refinement Of Protein Crystal Structures: Validation And Application.
Structure V. 15 1040 2007
PubMed-ID: 17850744  |  Reference-DOI: 10.1016/J.STR.2007.06.019

(-) Compounds

Molecule 1 - PUTATIVE TROPINONE REDUCTASE HOMOLOG AT1G07440
    Chains: A
    EC Number: 1.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PVP-13 (PQE DERIVATIVE)
    Expression System Strain: B834(DE3) P(LACI+RARE)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AT1G07440, F22G5_16, F22G5.20, F22G5.39
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Strain: CV. COLUMBIA

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit (8x): A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2Q45)

(-) Sites  (0, 0)

(no "Site" information available for 2Q45)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q45)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Q45)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q45)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_SHORTPS00061 Short-chain dehydrogenases/reductases family signature.TRNH2_ARATH146-174  1A:150-179
TRNH1_ARATH151-179  1A:161-179
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_SHORTPS00061 Short-chain dehydrogenases/reductases family signature.TRNH2_ARATH146-174  1A:150-179
TRNH1_ARATH151-179  1A:161-179

(-) Exons   (0, 0)

(no "Exon" information available for 2Q45)

(-) 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:218
 aligned with TRNH1_ARATH | P0DKI3 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:259
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256         
          TRNH1_ARATH     7 SQRWSLKAKTVLVTGGTKGIGHAIVEEFAGFGAVIHTCARNEYELNECLSKWQKKGFQVTGSVCDASLRPEREKLMQTVSSMFGGKLDILINNLGAIRSKPTLDYTAEDFSFHISTNLESAYHLSQLAHPLLKASGCGNIIFMSSIAGVVSASVGSIYSATKGALNQLARNLACEWASDGIRANAVAPAVIATPLAEAVYDDEFKKVVISRKPLGRFGEPEEVSSLVAFLCMPAASYITGQTICVDGGLTVNGFSYQPQ 265
               SCOP domains d2q45a_ A: automated matches                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2q45A00 A:7-265 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                 CATH domains
               Pfam domains --------------adh_short_C2-2q45A01 A:21-256                                                                                                                                                                                                               --------- Pfam domains
         Sec.struct. author hhhhh....eeee....hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhh....eeeee...------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.----------.hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.....-------------------------.hhhhhhhhhhhhhhhhhh.....eee....eee..eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:161-179    -------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q45 A   7 SQRWSLKAKTVLVTGGTKGIGHAIVEEFAGFGAVIHTCARNEYELNECLSKWQKKGFQVTGSVCDASLRPEREKLMQTVSSMFGGKLDILINNLGA------LDYTAEDFSFHISTNLESAYHLSQLAHPLLKASGCGNIIFMS----------GSIYSATKGALNQLARNLACEWASDGIRANAVAPAVIA-------------------------GEPEEVSSLVAFLCMPAASYITGQTICVDGGLTVNGFSYQPQ 265
                                    16        26        36        46        56        66        76        86        96     |   -  |    116       126       136       146   |     -    |  166       176       186       196 |       -         -       226       236       246       256         
                                                                                                                         102    109                                      150        161                                  198                       224                                         


Chain A from PDB  Type:PROTEIN  Length:218
 aligned with TRNH2_ARATH | Q8RX32 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:259
                                                                                                                                                                                                                                                                                           260 
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       | 
          TRNH2_ARATH     3 INRWSLQGMTALVTGGSKGIGYAIVEELVGFGARVHICDIDETLLNECLSGWHAKGFEVSGSICDVSSRPQRVQLMQTVSSLFGAKLNILINNVGKYILKPTLESTAEDFSSLMATNLESAYYISQLAHPLLKASGNGNIVFISSVTGVVSGTSTIYGVTKGALNQLARDLACEWASDNIRANSVAPWVTATSLVQKYLEDEIFAEAMFSRTPLGRACEPREVASLVTFLCLPAASYITGQTICIDGGFTVNGFSYKP-   -
               SCOP domains d2q45a_ A: automated matches                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2q45A00 A:7-265 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                 CATH domains
               Pfam domains --------------adh_short_C2-2q45A01 A:21-256                                                                                                                                                                                                               --------- Pfam domains
         Sec.struct. author hhhhh....eeee....hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhh....eeeee...------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.---------.hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.....--------------------------.hhhhhhhhhhhhhhhhhh.....eee....eee..eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:150-179    --------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q45 A   7 SQRWSLKAKTVLVTGGTKGIGHAIVEEFAGFGAVIHTCARNEYELNECLSKWQKKGFQVTGSVCDASLRPEREKLMQTVSSMFGGKLDILINNLGA------LDYTAEDFSFHISTNLESAYHLSQLAHPLLKASGCGNIIFMS---------GSIYSATKGALNQLARNLACEWASDGIRANAVAPAVIA--------------------------GEPEEVSSLVAFLCMPAASYITGQTICVDGGLTVNGFSYQPQ 265
                                    16        26        36        46        56        66        76        86        96     |   -  |    116       126       136       146   |     -   |   167       177       187       197|        -         -       226       236       246       256         
                                                                                                                         102    109                                      150       161                                  198                        224
   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, 1)

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

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (2, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (TRNH1_ARATH | P0DKI3)
molecular function
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

Chain A   (TRNH2_ARATH | Q8RX32)
molecular function
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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  2q45
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        TRNH1_ARATH | P0DKI3: 1xq1
        TRNH2_ARATH | Q8RX32: 1xq1

(-) Related Entries Specified in the PDB File

1xq1 ORIGINAL REFINEMENT BASED ON SAME DATA AND R-FREE SET.