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- PDB-4iph: Structure of N-terminal domain of RPA70 in complex with VU079104 ... -

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Basic information

Entry
Database: PDB / ID: 4iph
TitleStructure of N-terminal domain of RPA70 in complex with VU079104 inhibitor
ComponentsReplication protein A 70 kDa DNA-binding subunit
KeywordsPROTEIN 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 / lateral element / single-stranded telomeric DNA binding / G-rich strand telomeric DNA binding / Removal of the Flap Intermediate / chromatin-protein adaptor activity / protein localization to site of double-strand break / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) ...protein localization to chromosome / DNA replication factor A complex / lateral element / single-stranded telomeric DNA binding / G-rich strand telomeric DNA binding / Removal of the Flap Intermediate / chromatin-protein adaptor activity / protein localization to site of double-strand break / 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 / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / hemopoiesis / Presynaptic phase of homologous DNA pairing and strand exchange / site of DNA damage / PCNA-Dependent Long Patch Base Excision Repair / Regulation of HSF1-mediated heat shock response / Activation of the pre-replicative complex / HSF1 activation / telomere maintenance via telomerase / mismatch repair / Activation of ATR in response to replication stress / SUMOylation of DNA damage response and repair proteins / homeostasis of number of cells within a tissue / 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 / male germ cell nucleus / nucleotide-excision repair / Fanconi Anemia Pathway / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / double-strand break repair via homologous recombination / base-excision repair / PML body / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / Meiotic recombination / DNA-templated DNA replication / 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 / in utero embryonic development / damaged DNA binding / chromosome, telomeric region / DNA replication / DNA repair / positive regulation of cell population proliferation / DNA damage response / chromatin binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Replication factor-A protein 1, N-terminal domain / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain ...Replication factor-A protein 1, N-terminal domain / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-1FJ / Replication protein A 70 kDa DNA-binding subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsFeldkamp, M.D. / Frank, A.O. / Vangamudi, B. / Fesik, S.W. / Chazin, W.J.
CitationJournal: 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
DepositionJan 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Feb 19, 2020Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Revision 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Replication protein A 70 kDa DNA-binding subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2733
Polymers13,4981
Non-polymers7752
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.270, 54.270, 54.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Replication protein A 70 kDa DNA-binding subunit / RP-A p70 / Replication factor A protein 1 / RF-A protein 1 / Single-stranded DNA-binding 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
#2: Chemical ChemComp-1FJ / ~{N}-(2,3-dimethylphenyl)-7-oxidanylidene-12-sulfanylidene-5,11-dithia-1,8-diazatricyclo[7.3.0.0^{2,6}]dodeca-2(6),3,9-triene-10-carboxamide


Mass: 387.499 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H13N3O2S3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 7, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.94→2.2209 Å / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.8.1_1168)model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.1_1168phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B29

2b29


Resolution: 1.94→31.276 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 32.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2735 408 4.72 %Random
Rwork0.1924 ---
all0.1963 ---
obs0.1963 8644 98.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.94→31.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms941 0 50 108 1099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071026
X-RAY DIFFRACTIONf_angle_d1.1661401
X-RAY DIFFRACTIONf_dihedral_angle_d13.258393
X-RAY DIFFRACTIONf_chiral_restr0.08159
X-RAY DIFFRACTIONf_plane_restr0.005177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-2.22090.31261120.22622734X-RAY DIFFRACTION99
2.2209-2.79780.28651420.21612640X-RAY DIFFRACTION96
2.7978-31.27980.25871540.17112862X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 7.4162 Å / Origin y: 8.5879 Å / Origin z: 11.5306 Å
111213212223313233
T0.1189 Å20.0058 Å20.0077 Å2-0.1311 Å20.005 Å2--0.1167 Å2
L1.139 °2-0.2272 °2-0.1694 °2-1.261 °2-0.6956 °2--0.8109 °2
S0.0471 Å °-0.091 Å °0.0603 Å °0.1142 Å °0.0117 Å °0.0322 Å °-0.0358 Å °0.1017 Å °-0.0479 Å °
Refinement TLS groupSelection details: all

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