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- PDB-8gj9: RAD51C N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 8gj9
TitleRAD51C N-terminal domain
ComponentsRAD51C
KeywordsDNA BINDING PROTEIN / DNA-binding DNA damage DNA repair ATP binding
Biological speciesAlvinella pompejana (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsArvai, A.S. / Tainer, J.A. / Williams, G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35CA220430 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA092584 United States
CitationJournal: Nat Commun / Year: 2023
Title: RAD51C-XRCC3 structure and cancer patient mutations define DNA replication roles.
Authors: Longo, M.A. / Roy, S. / Chen, Y. / Tomaszowski, K.H. / Arvai, A.S. / Pepper, J.T. / Boisvert, R.A. / Kunnimalaiyaan, S. / Keshvani, C. / Schild, D. / Bacolla, A. / Williams, G.J. / Tainer, J.A. / Schlacher, K.
History
DepositionMar 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RAD51C
B: RAD51C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8533
Polymers14,7872
Non-polymers651
Water3,693205
1
A: RAD51C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4592
Polymers7,3941
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RAD51C


Theoretical massNumber of molelcules
Total (without water)7,3941
Polymers7,3941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.607, 45.607, 111.412
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-272-

HOH

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Components

#1: Protein RAD51C


Mass: 7393.551 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alvinella pompejana (invertebrata) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / Details: 0.05 mM Zn acetate 20% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 18437 / % possible obs: 99.8 % / Redundancy: 10.2 % / Biso Wilson estimate: 22.83 Å2 / Rsym value: 0.064 / Net I/σ(I): 59.5
Reflection shellResolution: 1.6→1.66 Å / Num. unique obs: 1803 / Rsym value: 0.648

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→32.22 Å / SU ML: 0.1612 / Cross valid method: FREE R-VALUE / σ(F): 0.17 / Phase error: 20.1637
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1928 875 4.96 %
Rwork0.1545 16750 -
obs0.1564 17625 95.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.91 Å2
Refinement stepCycle: LAST / Resolution: 1.6→32.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 1 205 1206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01421051
X-RAY DIFFRACTIONf_angle_d1.21371419
X-RAY DIFFRACTIONf_chiral_restr0.0762169
X-RAY DIFFRACTIONf_plane_restr0.011182
X-RAY DIFFRACTIONf_dihedral_angle_d14.8773409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.70.2541330.19042562X-RAY DIFFRACTION89.62
1.7-1.830.21281350.17352657X-RAY DIFFRACTION92.73
1.83-2.020.22211450.15532732X-RAY DIFFRACTION95.42
2.02-2.310.18171480.14172841X-RAY DIFFRACTION97.9
2.31-2.910.20151520.16432893X-RAY DIFFRACTION98.74
2.91-32.220.18011620.14893065X-RAY DIFFRACTION99.2

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