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Yorodumi- PDB-1bix: THE CRYSTAL STRUCTURE OF THE HUMAN DNA REPAIR ENDONUCLEASE HAP1 S... -
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-Basic information
Entry | Database: PDB / ID: 1bix | ||||||
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Title | THE CRYSTAL STRUCTURE OF THE HUMAN DNA REPAIR ENDONUCLEASE HAP1 SUGGESTS THE RECOGNITION OF EXTRA-HELICAL DEOXYRIBOSE AT DNA ABASIC SITES | ||||||
Components | AP ENDONUCLEASE 1 | ||||||
Keywords | DNA REPAIR / ENDONUCLEASE / HAP1 / REF-1 / ABASIC SITE RECOGNITION | ||||||
Function / homology | Function and homology information Resolution of Abasic Sites (AP sites) / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / site-specific endodeoxyribonuclease activity, specific for altered base / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded telomeric DNA binding / phosphodiesterase I activity / double-stranded DNA 3'-5' DNA exonuclease activity ...Resolution of Abasic Sites (AP sites) / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / site-specific endodeoxyribonuclease activity, specific for altered base / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded telomeric DNA binding / phosphodiesterase I activity / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / positive regulation of gene expression via chromosomal CpG island demethylation / Displacement of DNA glycosylase by APEX1 / phosphoric diester hydrolase activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / uracil DNA N-glycosylase activity / DNA catabolic process / 3'-5'-DNA exonuclease activity / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / DNA-(apurinic or apyrimidinic site) endonuclease activity / regulation of mRNA stability / 3'-5' exonuclease activity / telomere maintenance / base-excision repair, gap-filling / cell redox homeostasis / DNA endonuclease activity / base-excision repair / chromatin DNA binding / transcription corepressor activity / RNA-DNA hybrid ribonuclease activity / regulation of apoptotic process / DNA recombination / endonuclease activity / chromosome, telomeric region / damaged DNA binding / transcription coactivator activity / oxidoreductase activity / ribosome / nuclear speck / DNA repair / centrosome / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MIR, ANOMALOUS SCATTERING / Resolution: 2.2 Å | ||||||
Authors | Gorman, M.A. / Morera, S. / Rothwell, D.G. / De La Fortelle, E. / Mol, C.D. / Tainer, J.A. / Hickson, I.D. / Freemont, P.S. | ||||||
Citation | Journal: EMBO J. / Year: 1997 Title: The crystal structure of the human DNA repair endonuclease HAP1 suggests the recognition of extra-helical deoxyribose at DNA abasic sites. Authors: Gorman, M.A. / Morera, S. / Rothwell, D.G. / de La Fortelle, E. / Mol, C.D. / Tainer, J.A. / Hickson, I.D. / Freemont, P.S. #1: Journal: Thesis, The Open University / Year: 1998 Title: Crystal Structure of the Human DNA Repair Enzyme Ap Endonuclease 1 Authors: Gorman, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bix.cif.gz | 72.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bix.ent.gz | 52.8 KB | Display | PDB format |
PDBx/mmJSON format | 1bix.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bix_validation.pdf.gz | 367.7 KB | Display | wwPDB validaton report |
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Full document | 1bix_full_validation.pdf.gz | 367.8 KB | Display | |
Data in XML | 1bix_validation.xml.gz | 7 KB | Display | |
Data in CIF | 1bix_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/1bix ftp://data.pdbj.org/pub/pdb/validation_reports/bi/1bix | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32287.680 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: P27695, DNA-(apurinic or apyrimidinic site) lyase | ||||||
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#2: Chemical | ChemComp-SM / #3: Chemical | ChemComp-PT / | #4: Water | ChemComp-HOH / | Compound details | THE STRUCTURE IS A 35 AMINO ACID TRUNCATED FORM OF THE 'NATIVE' MOLECULE. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.4 / Details: pH 7.4 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: drop consists of equal volume of protein and reservoir solutions | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Dec 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 15089 / % possible obs: 98.1 % / Observed criterion σ(I): 2.2 / Redundancy: 3.6 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.19→2.31 Å / Redundancy: 3 % / Rmerge(I) obs: 0.114 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.114 / % possible all: 90 |
Reflection | *PLUS Num. measured all: 54729 |
Reflection shell | *PLUS % possible obs: 90 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR, ANOMALOUS SCATTERING / Resolution: 2.2→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: UNRESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 15.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.84 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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