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- PDB-4r4q: Crystal structure of RPA70N in complex with 5-(3-((N-(4-(5-carbox... -

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Basic information

Entry
Database: PDB / ID: 4r4q
TitleCrystal structure of RPA70N in complex with 5-(3-((N-(4-(5-carboxyfuran-2-yl)benzyl)acetamido)methyl)phenyl)-1-(3,4-dichlorophenyl)-1H-pyrazole-3-carboxylic acid
ComponentsReplication protein A 70 kDa DNA-binding subunitDNA replication
KeywordsPROTEIN BINDING / OB-fold / Protein-Protein Interaction
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 / double-strand break repair via homologous recombination / Translesion Synthesis by POLH / 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 / chromosome, telomeric region / damaged DNA binding / DNA repair / DNA damage response / nucleoplasm / metal ion binding / 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-3HZ / Replication protein A 70 kDa DNA-binding subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PDB entry 4IPC / Resolution: 1.35 Å
AuthorsFeldkamp, M.D. / Waterson, A.G. / Kennedy, J.P. / Patrone, J.D. / Pelz, N.F. / Frank, A.O. / Vangamudi, B. / Sousa-Fagundes, E.M. / Rossanese, O.W. / Fesik, S.W. / Chazin, W.J.
CitationJournal: ACS Med Chem Lett / Year: 2015
Title: Diphenylpyrazoles as replication protein a inhibitors.
Authors: Waterson, A.G. / Kennedy, J.P. / Patrone, J.D. / Pelz, N.F. / Feldkamp, M.D. / Frank, A.O. / Vangamudi, B. / Souza-Fagundes, E.M. / Rossanese, O.W. / Chazin, W.J. / Fesik, S.W.
History
DepositionAug 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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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)14,1022
Polymers13,4981
Non-polymers6041
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.161, 53.934, 53.975
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 / DNA replication / RP-A p70 / Replication factor A protein 1 / RF-A protein 1 / Single-stranded DNA-binding protein / ...RP-A p70 / Replication factor A protein 1 / RF-A protein 1 / Single-stranded DNA-binding protein / Replication protein A 70 kDa DNA-binding subunit / N-terminally processed


Mass: 13497.728 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-120) / 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-3HZ / 5-[4-({acetyl[4-(5-carboxyfuran-2-yl)benzyl]amino}methyl)phenyl]-1-(3,4-dichlorophenyl)-1H-pyrazole-3-carboxylic acid


Mass: 604.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H23Cl2N3O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.06 Å3/Da / Density % sol: 40.22 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM MES, 200 mM Calcium Acetate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 25, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.35→31.16 Å / Num. obs: 25127 / % possible obs: 97.64 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 22 Å2 / Rsym value: 0.067 / Net I/σ(I): 15.39
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 3.04 / Num. unique all: 2469 / Rsym value: 0.512 / % possible all: 97.64

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.9_1692)model building
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: PDB entry 4IPC / Resolution: 1.35→31.16 Å / SU ML: 0.12 / σ(F): 1.36 / Phase error: 17.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.188 1283 5.11 %RANDOM
Rwork0.1482 ---
obs0.1501 25098 99.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→31.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms920 0 42 127 1089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0211030
X-RAY DIFFRACTIONf_angle_d1.8691414
X-RAY DIFFRACTIONf_dihedral_angle_d15.143401
X-RAY DIFFRACTIONf_chiral_restr0.101166
X-RAY DIFFRACTIONf_plane_restr0.009183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.40180.25681470.18892537X-RAY DIFFRACTION98
1.4018-1.46560.19861450.15322618X-RAY DIFFRACTION100
1.4656-1.54290.20451370.13912636X-RAY DIFFRACTION100
1.5429-1.63960.19341560.13262609X-RAY DIFFRACTION100
1.6396-1.76610.20731340.13372636X-RAY DIFFRACTION100
1.7661-1.94380.19541400.13112675X-RAY DIFFRACTION100
1.9438-2.22510.15031480.12652623X-RAY DIFFRACTION100
2.2251-2.8030.17061460.15152701X-RAY DIFFRACTION100
2.803-31.1680.20111300.16132809X-RAY DIFFRACTION98

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