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Yorodumi- PDB-1hd7: A Second Divalent Metal Ion in the Active Site of a New Crystal F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hd7 | ||||||
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Title | A Second Divalent Metal Ion in the Active Site of a New Crystal Form of Human Apurinic/Apyridinimic Endonuclease, Ape1, and its Implications for the Catalytic Mechanism | ||||||
Components | DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE | ||||||
Keywords | DNA REPAIR / ENDONUCLEASE / APE1 / HAP1 / REF-1 | ||||||
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 / double-stranded DNA 3'-5' DNA exonuclease activity / phosphodiesterase I 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 / double-stranded DNA 3'-5' DNA exonuclease activity / phosphodiesterase I 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 / chromosome, telomeric region / endonuclease activity / DNA recombination / regulation of apoptotic process / transcription coactivator activity / damaged DNA binding / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Beernink, P.T. / Segelke, B.W. / Rupp, B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Two Divalent Metal Ions in the Active Site of a New Crystal Form of Human Apurinic/Apyrimidinic Endonuclease, Ape1: Implications for the Catalytic Mechanism Authors: Beernink, P.T. / Segelke, B.W. / Hadi, M.Z. / Erzberger, J.P. / Wilson III, D.M. / Rupp, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hd7.cif.gz | 73.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hd7.ent.gz | 54 KB | Display | PDB format |
PDBx/mmJSON format | 1hd7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hd7_validation.pdf.gz | 417 KB | Display | wwPDB validaton report |
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Full document | 1hd7_full_validation.pdf.gz | 425 KB | Display | |
Data in XML | 1hd7_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 1hd7_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/1hd7 ftp://data.pdbj.org/pub/pdb/validation_reports/hd/1hd7 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35606.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: ALL / Cell: ALL / Organelle: NUCLEUS / Plasmid: PET11D / Gene (production host): APE1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P27695, DNA-(apurinic or apyrimidinic site) lyase |
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#2: Chemical | ChemComp-PB / |
#3: Water | ChemComp-HOH / |
Compound details | ENDONUCLEOLYTIC CLEAVAGE NEAR APURINIC OR APYRIMIDINIC SITES TO PRODUCTS WITH 5'-PHOSPHATE. REPAIRS ...ENDONUCLEO |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % | |||||||||||||||||||||||||
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Crystal grow | pH: 4.5 Details: 0.1M NAOAC PH 4.6, 25% PEG 4K, 1 MM PB(II)OAC, 10-12 MG/ML PROTEIN. | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 4.6 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.2398 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 15, 1999 / Details: DUAL CRYSTAL MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2398 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→25 Å / Num. obs: 34905 / % possible obs: 99.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 29.68 Å2 / Rsym value: 0.082 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 1.95→2.01 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.5 / % possible all: 99.2 |
Reflection | *PLUS Num. measured all: 91465 / Rmerge(I) obs: 0.074 |
Reflection shell | *PLUS % possible obs: 99.3 % / Rmerge(I) obs: 0.471 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: TO BE PUBLISHED Resolution: 1.95→25 Å / SU B: 3.7 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.16
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Displacement parameters | Biso mean: 37.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→25 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.205 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |