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Yorodumi- PDB-3kdf: X-ray Crystal Structure of the Human Replication Protein A Comple... -
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-Basic information
Entry | Database: PDB / ID: 3kdf | ||||||
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Title | X-ray Crystal Structure of the Human Replication Protein A Complex from Wheat Germ Cell Free Expression | ||||||
Components |
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Keywords | REPLICATION / Wheat germ cell free / protein complex / Center for Eukaryotic Structural Genomics / PSI / replication protein A / Homo sapiens / Protein Structure Initiative / CESG / Acetylation / Alternative splicing / DNA replication / Nucleus / Phosphoprotein / Polymorphism | ||||||
Function / homology | Function and homology information protein localization to chromosome / DNA replication factor A complex / regulation of DNA damage checkpoint / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 ...protein localization to chromosome / DNA replication factor A complex / regulation of DNA damage checkpoint / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / regulation of double-strand break repair via homologous recombination / telomeric DNA binding / Presynaptic phase of homologous DNA pairing and strand exchange / Activation of the pre-replicative complex / PCNA-Dependent Long Patch Base Excision Repair / Regulation of HSF1-mediated heat shock response / HSF1 activation / mismatch repair / Activation of ATR in response to replication stress / mitotic G1 DNA damage checkpoint signaling / regulation of mitotic cell cycle / telomere maintenance / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Fanconi Anemia Pathway / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / double-strand break repair via homologous recombination / base-excision repair / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / Dual Incision in GG-NER / PML body / Meiotic recombination / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / site of double-strand break / single-stranded DNA binding / regulation of cell population proliferation / Processing of DNA double-strand break ends / protein phosphatase binding / DNA replication / Regulation of TP53 Activity through Phosphorylation / chromosome, telomeric region / damaged DNA binding / nuclear body / DNA repair / ubiquitin protein ligase binding / chromatin / enzyme binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.975 Å | ||||||
Authors | Burgie, E.S. / Bingman, C.A. / Phillips Jr., G.N. / Fox, B.G. / Makino, S.-I. / Center for Eukaryotic Structural Genomics (CESG) | ||||||
Citation | Journal: To be Published Title: X-ray Crystal Structure of the Human Replication Protein A Complex from Wheat Germ Cell Free Expression Authors: Makino, S.-I. / Burgie, E.S. / Bingman, C.A. / Fox, B.G. / Phillips Jr., G.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kdf.cif.gz | 214.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kdf.ent.gz | 180.2 KB | Display | PDB format |
PDBx/mmJSON format | 3kdf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kdf_validation.pdf.gz | 471.9 KB | Display | wwPDB validaton report |
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Full document | 3kdf_full_validation.pdf.gz | 479.9 KB | Display | |
Data in XML | 3kdf_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 3kdf_validation.cif.gz | 32.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/3kdf ftp://data.pdbj.org/pub/pdb/validation_reports/kd/3kdf | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 13774.071 Da / Num. of mol.: 2 / Mutation: M1S Source method: isolated from a genetically manipulated source Details: co-expressed with entity 1 / Source: (gene. exp.) Homo sapiens (human) / Description: Wheat Germ / Gene: REPA3, RPA14, RPA3 / Plasmid: pEU-His-Flexi / Production host: cell-free synthesis (others) / References: UniProt: P35244 #2: Protein | Mass: 14982.417 Da / Num. of mol.: 2 / Fragment: Residues 41-172 / Mutation: A41S Source method: isolated from a genetically manipulated source Details: co-expressed with entity 2 / Source: (gene. exp.) Homo sapiens (human) / Description: Wheat Germ / Gene: REPA2, RPA2, RPA32, RPA34 / Plasmid: pEU-His-Flexi / Production host: cell-free synthesis (others) / References: UniProt: P15927 #3: Chemical | ChemComp-EDO / #4: 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: 2.73 Å3/Da / Density % sol: 54.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 11% PEG 8000, 50 mM BisTris-propane pH 7.0, 50 mM NaCl, 5 mM HEPES pH 7.0, 0.3 mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9686, 0.97947 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 5, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Redundancy: 13.6 % / Av σ(I) over netI: 29.77 / Number: 595468 / Rmerge(I) obs: 0.101 / Χ2: 1.64 / D res high: 1.97 Å / D res low: 50 Å / Num. obs: 43894 / % possible obs: 97.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.97→50 Å / Num. obs: 43894 / % possible obs: 97.9 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.101 / Χ2: 1.643 / Net I/σ(I): 12.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.97→2 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.566 / Num. unique all: 1813 / Χ2: 1.134 / % possible all: 82.7 |
-Phasing
Phasing | Method: MAD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing MAD set |
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Phasing MAD set shell |
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