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(-) Description

Title :  CRYSTAL STRUCTURE OF CHROMATIN PROTEIN ALBA FROM HYPERTHERMOPHILIC ARCHAEON PYROCOCCUS HORIKOSHII
 
Authors :  K. Hada, T. Nakashima, T. Osawa, H. Shimada, Y. Kakuta, M. Kimura
Date :  17 Aug 07  (Deposition) - 05 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Alba, Dna/Rna Binding, Acetylation, Cytoplasm, Dna-Binding, Rna-Binding, Dna Binding Protein, Rna Binding Protein, Dna Binding Protein, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Hada, T. Nakashima, T. Osawa, H. Shimada, Y. Kakuta, M. Kimura
Crystal Structure And Functional Analysis Of An Archaeal Chromatin Protein Alba From The Hyperthermophilic Archaeon Pyrococcus Horikoshii Ot3.
Biosci. Biotechnol. Biochem. V. 72 749 2008
PubMed-ID: 18323660  |  Reference-DOI: 10.1271/BBB.70639
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA/RNA-BINDING PROTEIN ALBA
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-22B
    Expression System Strain: BL21(DE3) CODONPLUS RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PHS053
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953
    Strain: OT3

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ARG2Mod. Amino AcidARGININE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ARG1Mod. Amino AcidARGININE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ARG1Mod. Amino AcidARGININE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:69 , ASN A:81 , THR A:82 , SER A:83 , ASP B:46 , GLU B:49 , ILE B:50 , HIS C:26BINDING SITE FOR RESIDUE ARG A 920
2AC2SOFTWAREHIS A:26 , HOH A:921 , THR C:69 , ASN C:81 , SER C:83 , HOH C:931 , ASP D:46 , GLU D:49BINDING SITE FOR RESIDUE ARG C 921

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z7C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Z7C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z7C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z7C)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z7C)

(-) 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:90
 aligned with ALBA_PYRHO | O74101 from UniProtKB/Swiss-Prot  Length:93

    Alignment length:90
                                                                                                                   93 
                                    14        24        34        44        54        64        74        84        |-
           ALBA_PYRHO     5 HVVYIGKKPVMNYVLAVITQFHEGAKEVSIKARGRAISRAVDVAEIVRNRFLKDDVDVKEIKIGTEELPTADGRTTNTSTIEIVLARKT-   -
               SCOP domains d2z7ca_ A: automated matches                                                               SCOP domains
               CATH domains 2z7cA00 A:5-93  [code=3.30.110.20, no name defined]                                      - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee....hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhh.....eeeeeeeeeeeee.....eeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 2z7c A   5 HVVYIGKKPVMNYVLAVITQFHEGAKEVSIKARGRAISRAVDVAEIVRNRFLKDDVDVKEIKIGTEELPTADGRTTNTSTIEIVLARKTR 920
                                    14        24        34        44        54        64        74        84       920
                                                                                                                   93|
                                                                                                                   920


Chain B from PDB  Type:PROTEIN  Length:89
 aligned with ALBA_PYRHO | O74101 from UniProtKB/Swiss-Prot  Length:93

    Alignment length:89
                                    14        24        34        44        54        64        74        84         
           ALBA_PYRHO     5 HVVYIGKKPVMNYVLAVITQFHEGAKEVSIKARGRAISRAVDVAEIVRNRFLKDDVDVKEIKIGTEELPTADGRTTNTSTIEIVLARKT  93
               SCOP domains d2z7cb_ B: automated matches                                                              SCOP domains
               CATH domains 2z7cB00 B:5-93  [code=3.30.110.20, no name defined]                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....hhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhh.....eeeeeeeeeeeeeee...eeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 2z7c B   5 HVVYIGKKPVMNYVLAVITQFHEGAKEVSIKARGRAISRAVDVAEIVRNRFLKDDVDVKEIKIGTEELPTADGRTTNTSTIEIVLARKT  93
                                    14        24        34        44        54        64        74        84         


Chain C from PDB  Type:PROTEIN  Length:90
 aligned with ALBA_PYRHO | O74101 from UniProtKB/Swiss-Prot  Length:93

    Alignment length:90
                                                                                                                   93 
                                    14        24        34        44        54        64        74        84        |-
           ALBA_PYRHO     5 HVVYIGKKPVMNYVLAVITQFHEGAKEVSIKARGRAISRAVDVAEIVRNRFLKDDVDVKEIKIGTEELPTADGRTTNTSTIEIVLARKT-   -
               SCOP domains d2z7cc_ C: automated matches                                                               SCOP domains
               CATH domains 2z7cC00 C:5-93  [code=3.30.110.20, no name defined]                                      - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee....hhhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhhhhhhhh....eeeeeeeeeeeeee.....eeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 2z7c C   5 HVVYIGKKPVMNYVLAVITQFHEGAKEVSIKARGRAISRAVDVAEIVRNRFLKDDVDVKEIKIGTEELPTADGRTTNTSTIEIVLARKTR 921
                                    14        24        34        44        54        64        74        84       921
                                                                                                                   93|
                                                                                                                   921


Chain D from PDB  Type:PROTEIN  Length:92
 aligned with ALBA_PYRHO | O74101 from UniProtKB/Swiss-Prot  Length:93

    Alignment length:92
                                    11        21        31        41        51        61        71        81        91  
           ALBA_PYRHO     2 TEEHVVYIGKKPVMNYVLAVITQFHEGAKEVSIKARGRAISRAVDVAEIVRNRFLKDDVDVKEIKIGTEELPTADGRTTNTSTIEIVLARKT  93
               SCOP domains d2z7cd_ D: automated matches                                                                 SCOP domains
               CATH domains 2z7cD00 D:2-93  [code=3.30.110.20, no name defined]                                          CATH domains
           Pfam domains (1) ---Alba-2z7cD01 D:5-69                                              ------------------------ Pfam domains (1)
           Pfam domains (2) ---Alba-2z7cD02 D:5-69                                              ------------------------ Pfam domains (2)
           Pfam domains (3) ---Alba-2z7cD03 D:5-69                                              ------------------------ Pfam domains (3)
           Pfam domains (4) ---Alba-2z7cD04 D:5-69                                              ------------------------ Pfam domains (4)
         Sec.struct. author ...eeee....hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhh....eeeeeeeeeeeeee.....eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 2z7c D   2 TEEHVVYIGKKPVMNYVLAVITQFHEGAKEVSIKARGRAISRAVDVAEIVRNRFLKDDVDVKEIKIGTEELPTADGRTTNTSTIEIVLARKT  93
                                    11        21        31        41        51        61        71        81        91
   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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: AlbA (7)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (ALBA_PYRHO | O74101)
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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  2z7c
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