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(-) Description

Title :  ENSEMBLE REFINEMENT OF THE PROTEIN CRYSTAL STRUCTURE OF SELENOMETHIONYL GENE PRODUCT FROM ARABIDOPSIS THALIANA AT5G02240 IN SPACE GROUP P21212
 
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,B  (16x)
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ensemble Refinement, Refinement Methodology Development, Nadp, Structural Genomics, Protein Structure Initiative, Psi, Center For Eukaryotic Structural Genomics, Cesg, Unknown Function (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 - PROTEIN AT5G02240
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PVP-17
    Expression System Strain: B834 P(RARE2)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AT5G02240, T7H20_290
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Strain: CV. COLUMBIA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit (16x): AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:11 , SER A:13 , GLY A:14 , ARG A:15 , THR A:16 , ARG A:38 , ASP A:56 , ILE A:57 , LEU A:76 , THR A:77 , SER A:78 , GLN A:103 , VAL A:131 , GLY A:132 , SER A:133 , LYS A:155 , ALA A:174 , GLY A:175 , LEU A:177 , ARG A:205 , HOH A:403 , HOH A:404 , HOH A:409BINDING SITE FOR RESIDUE NAP A 400
2AC2SOFTWAREGLY B:14 , ARG B:15 , THR B:16 , ARG B:38 , ASP B:56 , ILE B:57 , LEU B:76 , THR B:77 , SER B:78 , VAL B:80 , GLN B:103 , GLY B:132 , SER B:133 , LYS B:155 , ALA B:174 , GLY B:175 , LEU B:177 , ARG B:205 , HOH B:402 , HOH B:404 , HOH B:422 , HOH B:434 , HOH B:508 , HOH B:511 , HOH B:514 , HOH B:520 , HOH B:541BINDING SITE FOR RESIDUE NAP B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q4B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Q4B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q4B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q4B)

(-) Exons   (0, 0)

(no "Exon" information available for 2Q4B)

(-) 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:243
 aligned with Y5224_ARATH | Q94EG6 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
          Y5224_ARATH     1 MANLPTVLVTGASGRTGQIVYKKLKEGSDKFVAKGLVRSAQGKEKIGGEADVFIGDITDADSINPAFQGIDALVILTSAVPKMKPGFDPTKGGRPEFIFEDGQYPEQVDWIGQKNQIDAAKVAGVKHIVVVGSMGGTNPDHPLNKLGNGNILVWKRKAEQYLADSGTPYTIIRAGGLLDKEGGVRELLVGKDDELLQTDTKTVPRADVAEVCIQALLFEEAKNKAFDLGSKPEGTSTPTKDFKALFSQVTSRF 253
               SCOP domains d2q4ba_ A: Hypothetical protein At5g02240 (T7H20_290)                                                                                                                                                                                                         SCOP domains
               CATH domains 2q4bA00 A:1-253 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...hhhhhhhhhhhh......eeeeee.hhhhhhhh.....eee....hhhhhhhhhh...eeee......ee.----------..ee.....hhhhhhhhhhhhhhhhhhhh...eeeeeee.......hhhhh....hhhhhhhhhhhhhhhh...eeeeee.eee........eeee..hhhhh....eeehhhhhhhhhhhhhhhhhh.eeeeeee..........hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q4b A   1 SANLPTVLVTGASGRTGQIVYKKLKEGSDKFVAKGLVRSAQGKEKIGGEADVFIGDITDADSINPAFQGIDALVILTSAVPKMK----------PEFIFEDGQYPEQVDWIGQKNQIDAAKVAGVKHIVVVGSMGGTNPDHPLNKLGNGNILVWKRKAEQYLADSGTPYTIIRAGGLLDKEGGVRELLVGKDDELLQTDTKTVPRADVAEVCIQALLFEEAKNKAFDLGSKPEGTSTPTKDFKALFSQVTSRF 253
                                    10        20        30        40        50        60        70        80   |     -    |  100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
                                                                                                              84         95                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:243
 aligned with Y5224_ARATH | Q94EG6 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
          Y5224_ARATH     1 MANLPTVLVTGASGRTGQIVYKKLKEGSDKFVAKGLVRSAQGKEKIGGEADVFIGDITDADSINPAFQGIDALVILTSAVPKMKPGFDPTKGGRPEFIFEDGQYPEQVDWIGQKNQIDAAKVAGVKHIVVVGSMGGTNPDHPLNKLGNGNILVWKRKAEQYLADSGTPYTIIRAGGLLDKEGGVRELLVGKDDELLQTDTKTVPRADVAEVCIQALLFEEAKNKAFDLGSKPEGTSTPTKDFKALFSQVTSRF 253
               SCOP domains d2q4bb_ B: Hypothetical protein At5g02240 (T7H20_290)                                                                                                                                                                                                         SCOP domains
               CATH domains 2q4bB00 B:1-253 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                           CATH domains
           Pfam domains (1) ------NAD_binding_10-2q4bB01 B:7-217                                                                                                                                                                                     ------------------------------------ Pfam domains (1)
           Pfam domains (2) ------NAD_binding_10-2q4bB02 B:7-217                                                                                                                                                                                     ------------------------------------ Pfam domains (2)
         Sec.struct. author .....eeeee.....hhhhhhhhhhhh....eeeeee.hhhhhhhh.....eee....hhhhhhhhhh...eeee......ee.----------..ee.....hhhhhhhhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.eee........eeee..hhhhhh...eeehhhhhhhhhhhhhhhhhh.eeeeeee..........hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q4b B   1 SANLPTVLVTGASGRTGQIVYKKLKEGSDKFVAKGLVRSAQGKEKIGGEADVFIGDITDADSINPAFQGIDALVILTSAVPKMK----------PEFIFEDGQYPEQVDWIGQKNQIDAAKVAGVKHIVVVGSMGGTNPDHPLNKLGNGNILVWKRKAEQYLADSGTPYTIIRAGGLLDKEGGVRELLVGKDDELLQTDTKTVPRADVAEVCIQALLFEEAKNKAFDLGSKPEGTSTPTKDFKALFSQVTSRF 253
                                    10        20        30        40        50        60        70        80   |     -    |  100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
                                                                                                              84         95
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Y5224_ARATH | Q94EG6)
biological process
    GO:0009737    response to abscisic 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 an abscisic acid stimulus.
cellular component
    GO:0048046    apoplast    The cell membranes and intracellular regions in a plant are connected through plasmodesmata, and plants may be described as having two major compartments: the living symplast and the non-living apoplast. The apoplast is external to the plasma membrane and includes cell walls, intercellular spaces and the lumen of dead structures such as xylem vessels. Water and solutes pass freely through it.
    GO:0009570    chloroplast stroma    The space enclosed by the double membrane of a chloroplast but excluding the thylakoid space. It contains DNA, ribosomes and some temporary products of photosynthesis.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0005774    vacuolar membrane    The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell.

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 Related Entries

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

UniProtKB/Swiss-Prot
        Y5224_ARATH | Q94EG6: 1xq6 1ybm 2q46

(-) Related Entries Specified in the PDB File

1xq6 NATIVE STRUCTURE OF AT5G02240 IN SPACE GROUP P21
1ybm ORIGINAL REFINEMENT BASED ON SAME DATA AND R-FREE SET.