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(-) Description

Title :  ENSEMBLE REFINEMENT OF THE PROTEIN CRYSTAL STRUCTURE OF AN ARABIDOPSIS THALIANA PUTATIVE STEROID SULPHOTRANSFERASE
 
Authors :  E. J. Levin, D. A. Kondrashov, G. E. Wesenberg, G. N. Phillips Jr. , Cent Eukaryotic Structural Genomics (Cesg)
Date :  30 May 07  (Deposition) - 19 Jun 07  (Release) - 29 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A  (16x)
Biol. Unit 1:  A  (2x)
Keywords :  Ensemble Refinement, Refinement Methodology Development, Steroid Sulphotransferase, Apo, Structural Genomics, Protein Structure Initiative, Psi, Center For Eukaryotic Structural Genomics, Cesg, Transferase (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
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FLAVONOL SULFOTRANSFERASE-LIKE
    ChainsA
    EC Number2.8.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPVP13
    Expression System StrainROSETTA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneAT2G03760, F19B11.21
    Organism CommonTHALE CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    Other DetailsAPO FORM
    StrainCV. COLUMBIA
    SynonymRARO47

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit (16x)A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1MLA1Ligand/IonMALONIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MLA1Ligand/IonMALONIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:45 , HIS A:46 , ILE A:50 , PRO A:74 , HIS A:140 , ILE A:201 , GLY A:202 , HOH A:934 , HOH A:1023 , HOH A:1027BINDING SITE FOR RESIDUE MLA A 901

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q3M)

(-) Cis Peptide Bonds  (2, 32)

Asymmetric Unit
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16Ser A:133 -Pro A:134
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16Gly A:203 -Pro A:204

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q3M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q3M)

(-) Exons   (0, 0)

(no "Exon" information available for 2Q3M)

(-) 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:284
 aligned with SOT12_ARATH | P52839 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:320
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325
          SOT12_ARATH     6 SVPAYLGDEDLTQETRALISSLPKEKGWLVSEIYEFQGLWHTQAILQGILICQKRFEAKDSDIILVTNPKSGTTWLKALVFALLNRHKFPVSSSGNHPLLVTNPHLLVPFLEGVYYESPDFDFSSLPSPRLMNTHISHLSLPESVKSSSCKIVYCCRNPKDMFVSLWHFGKKLAPEETADYPIEKAVEAFCEGKFIGGPFWDHILEYWYASRENPNKVLFVTYEELKKQTEVEMKRIAEFLECGFIEEEEVREIVKLCSFESLSNLEVNKEGKLPNGIETKTFFRKGEIGGWRDTLSESLAEEIDRTIEEKFKGSGLKFS 325
               SCOP domains d2q3ma_ A: automated matches                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2q3mA00 A:6-325 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh....hhhhh...........eee..eeehhhhhhhhhhhh..........eee......hhhhhhhhhhhhh.......hhhhhhhhh.hhhhhh.hhhhhhhhh...hhhhh.....eee.......hhhhhhh...eeeee.hhhhhhhhhhhhhhhh-------.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh-----------------------------hhhhh.hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q3m A   6 SVPAYLGDEDLTQETRALISSLPKEKGWLVSEIYEFQGLWHTQAILQGILICQKRFEAKDSDIILVTNPKSGTTWLKALVFALLNRHKFPVSSSGNHPLLVTNPHLLVPFLEGVYYESPDFDFSSLPSPRLMNTHISHLSLPESVKSSSCKIVYCCRNPKDMFVSLWHFGKKL-------YPIEKAVEAFCEGKFIGGPFWDHILEYWYASRENPNKVLFVTYEELKKQTEVEMKRIAEFLECGFIEEEEVREIVKLCSFE-----------------------------GWRDTLSESLAEEIDRTIEEKFKGSGLKFS 325
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175  |      -|      195       205       215       225       235       245       255       265|        -         -         -|      305       315       325
                                                                                                                                                                                                      178     186                                                                             266                           296                             

   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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Q3M)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (SOT12_ARATH | P52839)
molecular function
    GO:0080118    brassinosteroid sulfotransferase activity    Catalysis of the reaction: a brassinosteroid + 3'-phosphoadenosine-5'-phosphosulfate = sulfated brassinosteroid + adenosine-3',5'-diphosphate. This reaction is the transfer of a sulfate group to the hydroxyl group of a brassinosteroid acceptor, producing the sulfated brassinosteroid derivative.
    GO:1990135    flavonoid sulfotransferase activity    Catalysis of the reaction: a flavonoid + 3'-phosphoadenosine-5'-phosphosulfate = sulfated flavonoid + adenosine-3',5'-diphosphate. This reaction is the transfer of a sulfate group to the hydroxyl group of a flavonoid acceptor, producing the sulfated flavonoid derivative.
    GO:0008146    sulfotransferase activity    Catalysis of the transfer of a sulfate group from 3'-phosphoadenosine 5'-phosphosulfate to the hydroxyl group of an acceptor, producing the sulfated derivative and 3'-phosphoadenosine 5'-phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0016131    brassinosteroid metabolic process    The chemical reactions and pathways involving brassinosteroids, any of a group of steroid derivatives that occur at very low concentrations in plant tissues and may have hormone-like effects.
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0009751    response to salicylic acid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a salicylic acid stimulus.
    GO:0009651    response to salt stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SOT12_ARATH | P528391q44

(-) Related Entries Specified in the PDB File

1q44 ORIGINAL REFINEMENT BASED ON SAME DATA AND R-FREE SET.