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- PDB-8gj8: RAD51C C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 8gj8
TitleRAD51C C-terminal domain
ComponentsRAD51C
KeywordsDNA BINDING PROTEIN / DNA-binding DNA damage DNA repair ATP binding
Function / homologyADENOSINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesAlvinella pompejana (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAD51C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5633
Polymers32,1121
Non-polymers4522
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.032, 96.032, 55.683
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-519-

HOH

21A-537-

HOH

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Components

#1: Protein RAD51C


Mass: 32111.686 Da / Num. of mol.: 1 / Fragment: C-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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.71 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: (25 mg/mL protein) crystallized in 1:1 protein:crystallization reagent (0.1 M Bis-TRIS pH 5.5, 0.3 M Na formate), with best diffraction achieved after additive screen optimization with 4% ...Details: (25 mg/mL protein) crystallized in 1:1 protein:crystallization reagent (0.1 M Bis-TRIS pH 5.5, 0.3 M Na formate), with best diffraction achieved after additive screen optimization with 4% 1,3-propanediol and 10 days of growth.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.3→36.36 Å / Num. obs: 13402 / % possible obs: 99.69 % / Redundancy: 2 % / Rsym value: 0.022 / Net I/σ(I): 15.3
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 1314 / Rsym value: 0.323

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→36.36 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 13.916 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.304 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23745 641 4.8 %RANDOM
Rwork0.18764 ---
obs0.19015 12763 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.916 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0.43 Å2-0 Å2
2---0.43 Å2-0 Å2
3---1.38 Å2
Refinement stepCycle: 1 / Resolution: 2.3→36.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 28 44 2085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192095
X-RAY DIFFRACTIONr_bond_other_d0.0010.022025
X-RAY DIFFRACTIONr_angle_refined_deg1.8561.9732851
X-RAY DIFFRACTIONr_angle_other_deg0.87634658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6735259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46724.31888
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.29815364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7961510
X-RAY DIFFRACTIONr_chiral_restr0.1090.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022322
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02475
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 47 -
Rwork0.271 922 -
obs--99.38 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.18249.7869-2.993717.9473-8.54144.7861-0.1733-0.49840.48310.88-0.0506-0.0208-0.7131-0.1770.22390.29820.113-0.08180.2142-0.04030.173361.029733.927822.2225
22.5814-0.426-0.04163.9587-0.20053.0554-0.04220.3293-0.042-0.2005-0.0572-0.32150.19880.24230.09940.1582-0.02850.0090.22540.02720.035252.449544.14640.8517
34.1837-1.11910.38475.7864-0.51263.8639-0.0571-0.0522-0.2070.25710.00860.10710.3099-0.13820.04850.1526-0.03790.00670.21290.00880.012644.801741.29169.0196
43.8696-3.23520.00337.77613.82685.8758-0.7096-0.6990.74230.74640.5089-0.1618-0.7307-0.51580.20060.44840.1257-0.10740.4264-0.07150.200743.814757.075416.8427
513.5894-3.3731-1.25655.51030.70990.15310.30620.36041.1215-0.6548-0.21360.079-0.1026-0.076-0.09260.70540.0980.04870.53480.06410.635547.734165.53575.5312
65.24530.83332.36185.0779-1.21713.61980.05250.27760.38820.0501-0.1122-0.2491-0.74790.1510.05970.1440.0040.02860.09020.04680.219254.631360.394-1.3446
79.11356.6764-0.179615.2512.76652.67850.11210.4440.2021-0.09050.0526-0.6748-0.0560.3128-0.16470.19140.03370.03450.2170.08370.092956.838453.9076-6.7932
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A74 - 85
2X-RAY DIFFRACTION2A86 - 178
3X-RAY DIFFRACTION3A179 - 240
4X-RAY DIFFRACTION4A241 - 276
5X-RAY DIFFRACTION5A277 - 302
6X-RAY DIFFRACTION6A303 - 326
7X-RAY DIFFRACTION7A327 - 345

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