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- PDB-4luv: Fragment-Based Discovery of a Potent Inhibitor of Replication Pro... -

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Basic information

Entry
Database: PDB / ID: 4luv
TitleFragment-Based Discovery of a Potent Inhibitor of Replication Protein A Protein-Protein Interactions
ComponentsReplication protein A 70 kDa DNA-binding subunit
KeywordsDNA BINDING protein/inhibitor / OB-FOLD / PROTEIN-PROTEIN INTERACTION / PROTEIN BINDING / DNA BINDING protein-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-1DZ / Chem-1XS / Replication protein A 70 kDa DNA-binding subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsFeldkamp, M.D. / Frank, A.O. / Kennedy, J.P. / Waterson, A.G. / Olejnczak, E.O. / Pelz, N.F. / Patrone, J.D. / Vangamudi, B. / Camper, D.V. / Rossanese, O.W. ...Feldkamp, M.D. / Frank, A.O. / Kennedy, J.P. / Waterson, A.G. / Olejnczak, E.O. / Pelz, N.F. / Patrone, J.D. / Vangamudi, B. / Camper, D.V. / Rossanese, O.W. / Fesik, S.W. / Chazin, W.J.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Discovery of a potent inhibitor of replication protein a protein-protein interactions using a fragment-linking approach.
Authors: Frank, A.O. / Feldkamp, M.D. / Kennedy, J.P. / Waterson, A.G. / Pelz, N.F. / Patrone, J.D. / Vangamudi, B. / Camper, D.V. / Rossanese, O.W. / Chazin, W.J. / Fesik, S.W.
History
DepositionJul 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...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 / 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)14,0173
Polymers13,4981
Non-polymers5192
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.971, 53.528, 54.046
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 / ...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: RPA70N (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): BL-21 DE3 / References: UniProt: P27694
#2: Chemical ChemComp-1XS / 5-(3-chloro-4-fluorophenyl)furan-2-carboxylic acid


Mass: 240.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H6ClFO3
#3: Chemical ChemComp-1DZ / 1-(3-methylphenyl)-5-phenyl-1H-pyrazole-3-carboxylic acid


Mass: 278.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.03 Å3/Da / Density % sol: 39.54 %
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: 0.97872 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 12, 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: 1.4→50 Å / Num. all: 213065 / Num. obs: 42059 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 12.56 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 15.53
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 6.61 / Num. unique all: 2188 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.8.2_1309)model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2B29

2b29


Resolution: 1.4→38.032 Å / SU ML: 0.11 / σ(F): 1.38 / Phase error: 16.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1696 1146 5.12 %RANDOM
Rwork0.1387 ---
obs0.1403 22385 99.67 %-
all-22426 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→38.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms941 0 37 102 1080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071129
X-RAY DIFFRACTIONf_angle_d1.3041562
X-RAY DIFFRACTIONf_dihedral_angle_d17.652469
X-RAY DIFFRACTIONf_chiral_restr0.073182
X-RAY DIFFRACTIONf_plane_restr0.005206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.460.191430.12492558X-RAY DIFFRACTION98
1.4607-1.53770.17581600.10752589X-RAY DIFFRACTION100
1.5377-1.6340.1841340.11012645X-RAY DIFFRACTION100
1.634-1.76020.17061240.11582637X-RAY DIFFRACTION100
1.7602-1.93730.15931410.11492662X-RAY DIFFRACTION100
1.9373-2.21770.15021570.1142640X-RAY DIFFRACTION100
2.2177-2.79390.17831490.15162690X-RAY DIFFRACTION100
2.7939-38.04590.17131380.16472818X-RAY DIFFRACTION99

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