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Yorodumi- PDB-3zvl: The structural basis for substrate recognition by mammalian polyn... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zvl | ||||||
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Title | The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase | ||||||
Components | BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE | ||||||
Keywords | HYDROLASE/TRANSFERASE / HYDROLASE-TRANSFERASE COMPLEX / BASE EXCISION REPAIR / BER / NON-HOMOLOGOUS END-JOINING / NHEJ / DNA REPAIR / CANCER | ||||||
Function / homology | Function and homology information polynucleotide 3'-phosphatase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase activity / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / DNA ligation involved in DNA repair / SCF ubiquitin ligase complex / positive regulation of double-strand break repair via nonhomologous end joining / protein K63-linked ubiquitination / positive regulation of telomere capping ...polynucleotide 3'-phosphatase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase activity / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / DNA ligation involved in DNA repair / SCF ubiquitin ligase complex / positive regulation of double-strand break repair via nonhomologous end joining / protein K63-linked ubiquitination / positive regulation of telomere capping / ubiquitin-like ligase-substrate adaptor activity / positive regulation of telomere maintenance via telomerase / double-strand break repair via nonhomologous end joining / site of double-strand break / double-stranded DNA binding / response to oxidative stress / phosphorylation / DNA repair / DNA damage response / nucleolus / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Garces, F. / Pearl, L.H. / Oliver, A.W. | ||||||
Citation | Journal: Mol.Cell / Year: 2011 Title: The Structural Basis for Substrate Recognition by Mammalian Polynucleotide Kinase 3' Phosphatase. Authors: Garces, F. / Pearl, L.H. / Oliver, A.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zvl.cif.gz | 105.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zvl.ent.gz | 77.3 KB | Display | PDB format |
PDBx/mmJSON format | 3zvl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/3zvl ftp://data.pdbj.org/pub/pdb/validation_reports/zv/3zvl | HTTPS FTP |
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-Related structure data
Related structure data | 3zvmC 3zvnC 1yj5S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 45948.227 Da / Num. of mol.: 1 Fragment: POLYNUCLEOTIDE 3'-PHOSPHATASE AND POLYNUCLEOTIDE 5'-HYDROXYL-KINASE DOMAINS, RESIDUES 111-522 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA2 (DE3) PLYSS References: UniProt: Q9JLV6, polynucleotide 3'-phosphatase, polynucleotide 5'-hydroxyl-kinase |
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-Non-polymers , 5 types, 523 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-ACT / #6: Water | ChemComp-HOH / | |
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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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | Details: 0.05 M NACACODYLATE PH 6.5, 0.2 M AMMONIUM ACETATE, 0.01 M MG ACETATE, 30 % (W/V) PEG 8000. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 22, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→33.93 Å / Num. obs: 39354 / % possible obs: 90.1 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 14.97 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.3 / % possible all: 58.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YJ5 Resolution: 1.65→33.933 Å / SU ML: 0.2 / σ(F): 0.84 / Phase error: 22.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.337 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.65→33.933 Å
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Refine LS restraints |
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LS refinement shell |
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