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(-) Description

Title :  ENSEMBLE REFINEMENT OF THE PROTEIN CRYSTAL STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT3G21360
 
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 :  2.39
Chains :  Asym. Unit :  A,B  (4x)
Biol. Unit 1:  A,B  (1x)
Keywords :  Ensemble Refinement, Refinement Methodology Development, At3G21360, 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
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CLAVAMINATE SYNTHASE-LIKE PROTEIN AT3G21360
    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: AT3G21360, MHC9_4
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Strain: CV. COLUMBIA

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2SO44Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:135 , THR A:147 , SER A:314 , ARG A:315 , ARG A:322BINDING SITE FOR RESIDUE SO4 A 801
2AC2SOFTWAREARG A:158 , LYS A:162 , LYS A:330 , HOH A:1044BINDING SITE FOR RESIDUE SO4 A 802
3AC3SOFTWAREHIS A:163 , PRO A:164 , GLU A:165 , PHE A:166 , HOH A:1086BINDING SITE FOR RESIDUE SO4 A 803
4AC4SOFTWAREHIS A:120 , GLU A:122 , HIS A:313 , HOH A:1131 , HOH A:1175BINDING SITE FOR RESIDUE FE A 901
5AC5SOFTWAREHIS B:163 , PRO B:164 , GLU B:165 , PHE B:166 , HOH B:1079BINDING SITE FOR RESIDUE SO4 B 804
6AC6SOFTWAREHIS B:120 , GLU B:122 , HIS B:313 , HOH B:1179 , HOH B:1180BINDING SITE FOR RESIDUE FE B 902

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q4A)

(-) Cis Peptide Bonds  (7, 28)

Asymmetric Unit
No.ModelResidues
11, 2, 3, 4Phe A:22 -Pro A:23
21, 2, 3, 4Gly A:231 -Pro A:232
31, 2, 3, 4Pro A:320 -Pro A:321
41, 2, 3, 4Phe B:22 -Pro B:23
51, 2, 3, 4Ile B:33 -Pro B:34
61, 2, 3, 4Gly B:231 -Pro B:232
71, 2, 3, 4Pro B:320 -Pro B:321

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q4A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q4A)

(-) Exons   (0, 0)

(no "Exon" information available for 2Q4A)

(-) 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:321
 aligned with Y3136_ARATH | Q9LIG0 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:327
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       
          Y3136_ARATH     4 LLLVETPIPQQKHYESKPFPAVISPPSASIPIPALSLPLFTQTIKTQKHYLDSLLHESGAVLFRGFPVNSADDFNDVVEAFGFDELPYVGGAAPRTSVVGRVFTANESPPDQKIPFHHEMAQVREFPSKLFFYCEIEPKCGGETPIVLSHVVYERMKDKHPEFVQRLEEHGLLYVRVLGEDDDPSSPIGRGWKSTFLTHDKNLAEQRAVDLGMKLEWTEDGGAKTVMGPIPAIKYDESRNRKVWFNSMVAAYTGWEDKRNDPRKAVTFGDGKPLPADIVHDCLRILEEECVAVPWQRGDVLLIDNWAVLHSRRPFDPPRRVLASLCK 330
               SCOP domains d2q4aa_ A: automated match      es                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee......eee..eee.eeee..------...hhhhhhhhhhhhhhhhhhhhhhhheeee......hhhhhhhhhhhh..............eeee..eee.........eeee...........eeeeeeee...ee....eeehhhhhhhhhhhhhhhhhhhhhhheeeeeee............hhhhhh...hhhhhhhhhhhh....ee.....eeeeeeee...eee....eee...hhhhhhh.......hhhhheee......hhhhhhhhhhhhhhhh.........eeeee...eeeee..ee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q4a A   4 LLLVETPIPQQKHYESKPFPAVISPP------PALSLPLFTQTIKTQKHYLDSLLHESGAVLFRGFPVNSADDFNDVVEAFGFDELPYVGGAAPRTSVVGRVFTANESPPDQKIPFHHEMAQVREFPSKLFFYCEIEPKCGGETPIVLSHVVYERMKDKHPEFVQRLEEHGLLYVRVLGEDDDPSSPIGRGWKSTFLTHDKNLAEQRAVDLGMKLEWTEDGGAKTVMGPIPAIKYDESRNRKVWFNSMVAAYTGWEDKRNDPRKAVTFGDGKPLPADIVHDCLRILEEECVAVPWQRGDVLLIDNWAVLHSRRPFDPPRRVLASLCK 330
                                    13        23     |   -  |     43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       
                                                    29     36                                                                                                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:322
 aligned with Y3136_ARATH | Q9LIG0 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:329
                                    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         
          Y3136_ARATH     2 AELLLVETPIPQQKHYESKPFPAVISPPSASIPIPALSLPLFTQTIKTQKHYLDSLLHESGAVLFRGFPVNSADDFNDVVEAFGFDELPYVGGAAPRTSVVGRVFTANESPPDQKIPFHHEMAQVREFPSKLFFYCEIEPKCGGETPIVLSHVVYERMKDKHPEFVQRLEEHGLLYVRVLGEDDDPSSPIGRGWKSTFLTHDKNLAEQRAVDLGMKLEWTEDGGAKTVMGPIPAIKYDESRNRKVWFNSMVAAYTGWEDKRNDPRKAVTFGDGKPLPADIVHDCLRILEEECVAVPWQRGDVLLIDNWAVLHSRRPFDPPRRVLASLCK 330
               SCOP domains d2q4ab_ B: automated matches                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------TauD-2q4aB01 B:18-329                                                                                                                                                                                                                                                                                                   - Pfam domains (1)
           Pfam domains (2) ----------------TauD-2q4aB02 B:18-329                                                                                                                                                                                                                                                                                                   - Pfam domains (2)
         Sec.struct. author .....eee.....eee..eee.eeee...........hhhhhhhhhhhhhhhhhhhhhhhheeee......hhhhhhhhhhhhh......-------.eee..eee.........eeee...........eeeeeeee...ee....eeehhhhhhhhhhhhhhhhhhhhhhheeeeeee............hhhhhh...hhhhhhhhhhhh..eee......eeeeeeee...eee....eee...hhhhhhhhh.....hhhh.eee......hhhhhhhhhhhhhhhh.........eeeee...eeeee..ee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q4a B   2 AELLLVETPIPQQKHYESKPFPAVISPPSASIPIPALSLPLFTQTIKTQKHYLDSLLHESGAVLFRGFPVNSADDFNDVVEAFGFDELPY-------TSVVGRVFTANESPPDQKIPFHHEMAQVREFPSKLFFYCEIEPKCGGETPIVLSHVVYERMKDKHPEFVQRLEEHGLLYVRVLGEDDDPSSPIGRGWKSTFLTHDKNLAEQRAVDLGMKLEWTEDGGAKTVMGPIPAIKYDESRNRKVWFNSMVAAYTGWEDKRNDPRKAVTFGDGKPLPADIVHDCLRILEEECVAVPWQRGDVLLIDNWAVLHSRRPFDPPRRVLASLCK 330
                                    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         
                                                                                                                    91      99
   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: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Q4A)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Y3136_ARATH | Q9LIG0)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
cellular component
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        Y3136_ARATH | Q9LIG0: 1y0z

(-) Related Entries Specified in the PDB File

1y0z ORIGINAL REFINEMENT BASED ON SAME DATA AND R-FREE SET.