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Yorodumi- PDB-4iph: Structure of N-terminal domain of RPA70 in complex with VU079104 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4iph | ||||||
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Title | Structure of N-terminal domain of RPA70 in complex with VU079104 inhibitor | ||||||
Components | Replication protein A 70 kDa DNA-binding subunitDNA replication | ||||||
Keywords | PROTEIN BINDING/INHIBITOR / OB-fold / PROTEIN BINDING / PROTEIN BINDING-INHIBITOR complex | ||||||
Function / homology | Function and homology information protein localization to chromosome / DNA replication factor A complex / chromatin-protein adaptor activity / protein localization to site of double-strand break / Removal of the Flap Intermediate / G-rich strand telomeric DNA binding / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / single-stranded telomeric DNA binding / Removal of the Flap Intermediate from the C-strand ...protein localization to chromosome / DNA replication factor A complex / chromatin-protein adaptor activity / protein localization to site of double-strand break / Removal of the Flap Intermediate / G-rich strand telomeric DNA binding / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / single-stranded telomeric DNA binding / Removal of the Flap Intermediate from the C-strand / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / site of DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / telomere maintenance via telomerase / PCNA-Dependent Long Patch Base Excision Repair / mismatch repair / Activation of the pre-replicative complex / Regulation of HSF1-mediated heat shock response / HSF1 activation / Activation of ATR in response to replication stress / SUMOylation of DNA damage response and repair proteins / telomere maintenance / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / meiotic cell cycle / Recognition of DNA damage by PCNA-containing replication complex / nucleotide-excision repair / Fanconi Anemia Pathway / 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 / DNA-templated DNA replication / 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 / single-stranded DNA binding / site of double-strand break / Processing of DNA double-strand break ends / DNA recombination / Regulation of TP53 Activity through Phosphorylation / DNA replication / damaged DNA binding / chromosome, telomeric region / DNA repair / DNA damage response / nucleoplasm / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | ||||||
Authors | Feldkamp, M.D. / Frank, A.O. / Vangamudi, B. / Fesik, S.W. / Chazin, W.J. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Surface Reengineering of RPA70N Enables Cocrystallization with an Inhibitor of the Replication Protein A Interaction Motif of ATR Interacting Protein. Authors: Feldkamp, M.D. / Frank, A.O. / Kennedy, J.P. / Patrone, J.D. / Vangamudi, B. / Waterson, A.G. / Fesik, S.W. / Chazin, W.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4iph.cif.gz | 68.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iph.ent.gz | 50.6 KB | Display | PDB format |
PDBx/mmJSON format | 4iph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/4iph ftp://data.pdbj.org/pub/pdb/validation_reports/ip/4iph | HTTPS FTP |
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-Related structure data
Related structure data | 4ipcC 4ipdC 4ipgC 2b29S C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 13497.728 Da / Num. of mol.: 1 / Mutation: E7R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RPA1, REPA1, RPA70 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: P27694 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.15 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM MES, 200 mM Calcium Acetate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97857 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 7, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→31.276 Å / Num. all: 49814 / Num. obs: 8663 / % possible obs: 98.31 % / Observed criterion σ(F): 1.94 / Observed criterion σ(I): 1.94 / Redundancy: 5.7 % / Biso Wilson estimate: 24.7 Å2 / Rsym value: 0.106 / Net I/σ(I): 14.33 |
Reflection shell | Resolution: 1.94→2.2209 Å / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B29 Resolution: 1.94→31.276 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 32.1 / 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 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94→31.276 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 7.4162 Å / Origin y: 8.5879 Å / Origin z: 11.5306 Å
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Refinement TLS group | Selection details: all |