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Yorodumi- PDB-1e9n: A second divalent metal ion in the active site of a new crystal f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1e9n | ||||||
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Title | A second divalent metal ion in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1, and its implications for the catalytic mechanism | ||||||
Components | DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE | ||||||
Keywords | DNA REPAIR / DNA REPAIR ENDONUCLEASE / BASE EXCISION REPAIR / ABASIC ENDONUCLEASE / APE1 / HAP1 / REF-1 / ALPHA / BETA SANDWICH | ||||||
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: 2.2 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 | 1e9n.cif.gz | 129 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e9n.ent.gz | 99.5 KB | Display | PDB format |
PDBx/mmJSON format | 1e9n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e9n_validation.pdf.gz | 432.2 KB | Display | wwPDB validaton report |
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Full document | 1e9n_full_validation.pdf.gz | 450.8 KB | Display | |
Data in XML | 1e9n_validation.xml.gz | 27.1 KB | Display | |
Data in CIF | 1e9n_validation.cif.gz | 38.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/1e9n ftp://data.pdbj.org/pub/pdb/validation_reports/e9/1e9n | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE BIOLOGICAL UNIT IS HALF OF THE ASYMMETRIC UNIT |
-Components
#1: Protein | Mass: 35606.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Gene: APE1 / 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 #2: Chemical | ChemComp-PB / #3: Water | ChemComp-HOH / | Compound details | ENDONUCLEO | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: HANGING DROP, DROP 2+2 UL, 15MG/ML PROTEIN, 1 ML WELL, 0.1M TRIS-HCL, PH 7.5, 0.2M NAOAC, 30% PEG4K, 20MM HECAMEG, 1MM PB(OAC)2, 1MM DTT | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / 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: BL11-1 / Wavelength: 1.2398 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 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: 2.2→67.42 Å / Num. obs: 34905 / % possible obs: 93 % / Redundancy: 2.9 % / Rsym value: 0.082 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 2 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 2.1 / % possible all: 70.5 |
Reflection | *PLUS Highest resolution: 2.2 Å / Num. measured all: 102875 / Rmerge(I) obs: 0.082 |
Reflection shell | *PLUS % possible obs: 70.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: TO BE PUBLISHED Resolution: 2.2→20 Å / Isotropic thermal model: TNT BCORREL V1.0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO_V012 / Details: NCS WEIGHT 60, THEN RELAXED AT END OF REFINEMENT
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Solvent computation | Solvent model: BABENET SCALING / Bsol: 150 Å2 / ksol: 0.8 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5F / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection Rfree: 3499 / Rfactor all: 0.186 / Rfactor Rfree: 0.252 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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