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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ARCHAEA SPECIFIC DNA BINDING PROTEIN
 
Authors :  T. S. Kumarevel, K. Sakamoto, A. Shinkai, S. Yokoyama, Riken Structur Genomics/Proteomics Initiative (Rsgi)
Date :  12 Jun 06  (Deposition) - 12 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Archaea, Aeropyrum Pernix, Dna Binding Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. S. Kumarevel, K. Sakamoto, A. Shinkai, S. Yokoyama
Crystal Structure Of The Archaea Specific Dna Binding Protein From Aeropyrum Pernix K1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA/RNA-BINDING PROTEIN ALBA 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 272557
    Strain: K1
    Synonym: DNA BINDING PROTEIN

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1EDO12Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:42 , ASN A:45 , ARG A:46 , HOH A:6040BINDING SITE FOR RESIDUE EDO A 1001
2AC2SOFTWAREMET A:17 , VAL A:20 , ARG A:40 , ARG A:57 , HOH A:6064 , HOH A:6081BINDING SITE FOR RESIDUE EDO A 2001
3AC3SOFTWARETHR A:26 , GLU A:29 , ILE A:74 , VAL A:76 , ARG A:84 , THR A:85BINDING SITE FOR RESIDUE EDO A 3001
4AC4SOFTWAREPRO A:15 , ARG A:46 , HOH A:6082BINDING SITE FOR RESIDUE EDO A 4001
5AC5SOFTWAREARG A:40 , ARG A:57 , HOH A:6003 , HOH A:6042 , HOH A:6044 , HOH A:6053BINDING SITE FOR RESIDUE EDO A 5001
6AC6SOFTWAREGLY A:12 , ARG A:13 , ARG A:57 , HOH A:6053BINDING SITE FOR RESIDUE EDO A 6001

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:3 -A:94

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2H9U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2H9U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2H9U)

(-) Exons   (0, 0)

(no "Exon" information available for 2H9U)

(-) 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:101
 aligned with ALBA2_AERPE | Q9YAX2 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:101
                                    11        21        31        41        51        61        71        81        91       101 
          ALBA2_AERPE     2 ACEGAPEVRIGRKPVMNYVLAILTTLMEQGTNQVVVKARGRNINRAVDAVEIVRKRFAKNIEIKDIKIDSQEIEVQTPEGQTRTRRVSSIEICLEKAGESA 102
               SCOP domains d2h9ua_ A: automated matches                                                                          SCOP domains
               CATH domains 2h9uA00 A:2-102  [code=3.30.110.20, no name defined]                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee....hhhhhhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhhhhh...eeeeeeeeeeeeeeee.....eeeeeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 2h9u A   2 ACEGAPEVRIGRKPVMNYVLAILTTLMEQGTNQVVVKARGRNINRAVDAVEIVRKRFAKNIEIKDIKIDSQEIEVQTPEGQTRTRRVSSIEICLEKAGESA 102
                                    11        21        31        41        51        61        71        81        91       101
   Legend:   → Mismatch (orange background)
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  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) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2H9U)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (ALBA2_AERPE | Q9YAX2)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    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

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        ALBA2_AERPE | Q9YAX2: 3u6y

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