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- PDB-8gja: RAD51C-XRCC3 structure -

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Basic information

Entry
Database: PDB / ID: 8gja
TitleRAD51C-XRCC3 structure
Components
  • RAD51C
  • XRCC3
KeywordsDNA BINDING PROTEIN / DNA-binding DNA damage DNA repair ATP binding
Function / homologyADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION
Function and homology information
Biological speciesAlvinella pompejana (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsArvai, A.S. / Tainer, J.A. / Williams, G. / Longo, M.A.
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 1.1Oct 18, 2023Group: Structure summary / Category: audit_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAD51C
B: XRCC3
C: RAD51C
D: XRCC3
E: RAD51C
F: XRCC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,21117
Polymers213,3176
Non-polymers2,89311
Water3,153175
1
A: RAD51C
B: XRCC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0926
Polymers71,1062
Non-polymers9864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RAD51C
D: XRCC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0926
Polymers71,1062
Non-polymers9864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: RAD51C
F: XRCC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0265
Polymers71,1062
Non-polymers9203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.940, 112.300, 259.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein RAD51C


Mass: 32077.500 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alvinella pompejana (invertebrata) / Production host: Escherichia coli (E. coli)
#2: Protein XRCC3


Mass: 39028.309 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alvinella pompejana (invertebrata) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: (25 mg/mL protein)+ 2.5 mM ADP601 BeF + 5mM MgCl2, grew with a 1:2 protein:crystallization reagent (1 M HEPES pH 7.5, 20% PEG 3,350, 2% Tacsimate pH 7.0,) ratio and reached maximum growth after 15 days.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 2.6→38.33 Å / Num. obs: 60211 / % possible obs: 99.9 % / Redundancy: 26.4 % / Biso Wilson estimate: 55.55 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.5
Reflection shellResolution: 2.6→2.67 Å / Num. unique obs: 4378 / CC1/2: 0.444

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→38.33 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2318 1865 3.33 %
Rwork0.1856 --
obs0.1871 56007 92.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→38.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14177 0 182 175 14534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.854
X-RAY DIFFRACTIONf_dihedral_angle_d15.8115425
X-RAY DIFFRACTIONf_chiral_restr0.0482344
X-RAY DIFFRACTIONf_plane_restr0.0052507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.670.36291210.31643414X-RAY DIFFRACTION77
2.67-2.750.33721200.28863591X-RAY DIFFRACTION81
2.75-2.840.32231370.26723741X-RAY DIFFRACTION85
2.84-2.940.30041300.24283882X-RAY DIFFRACTION88
2.94-3.060.30731390.23154066X-RAY DIFFRACTION92
3.06-3.20.28221450.22984181X-RAY DIFFRACTION94
3.2-3.370.25911430.20914278X-RAY DIFFRACTION96
3.37-3.580.22451500.17764336X-RAY DIFFRACTION97
3.58-3.850.2041540.1744405X-RAY DIFFRACTION98
3.85-4.240.21841510.1614436X-RAY DIFFRACTION99
4.24-4.850.18991550.13864510X-RAY DIFFRACTION100
4.85-6.110.22391560.18054546X-RAY DIFFRACTION100
6.11-38.330.20161640.17184756X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.23-0.1692-0.05150.1943-0.07790.06240.4622-0.06310.32660.2271-0.15840.3062-0.31360.11710.01310.3988-0.0520.08720.3904-0.12780.5056-7.5376109.3498114.849
20.6394-0.21520.04880.13680.15720.67690.11770.34970.5099-0.05860.22020.40250.0642-0.24990.15690.30210.03370.03720.36910.10090.5966-7.7149108.8651102.0824
30.05370.001-0.06350.3683-0.44260.55620.27020.08960.4930.01160.14390.0675-0.66270.08140.87480.5358-0.04610.26980.3579-0.15810.83191.6455123.6724109.6575
40.05760.1373-0.06190.3852-0.12650.22820.508-0.82130.85760.9493-0.5220.9924-0.55720.222-0.01410.7652-0.15630.4391-0.4769-0.78430.92790.1921124.5899118.5676
50.8528-0.39950.92680.5622-0.51411.26050.8175-0.8834-0.28010.464-0.2360.11830.4397-0.03130.71510.4665-0.24840.17290.6179-0.11370.19841.3589105.8492122.4486
60.08590.0868-0.09710.0893-0.10230.1086-0.2832-0.17580.4808-0.066-0.27680.1550.243-0.0931-0.05661.0047-0.2859-0.37410.94030.16180.8743-2.4267101.7779130.3951
70.3210.06560.1250.0320.11290.1455-0.14850.5044-0.33310.19230.10310.2829-0.0492-0.1182-0.07891.10120.26990.42070.1289-0.04951.9886-6.1351144.3103.9429
80.85520.4611-0.74541.1214-0.60890.66330.13480.1379-0.0324-0.0455-0.1107-0.03530.06080.07150.00570.33470.0424-0.01130.34070.05290.326723.4717109.824593.8367
92.0089-0.69290.19091.2019-0.77730.56240.0133-0.43040.49560.6911-0.1422-0.16-0.59230.1682-0.01180.5131-0.07370.03540.39660.03910.429828.2957123.6079102.6049
101.96140.0672-0.51180.7492-0.24071.3140.2965-0.8620.22670.3094-0.1193-0.0062-0.45770.11330.27640.5106-0.07710.0010.58020.01610.349722.53116.0746111.2564
110.5926-0.6082-0.47070.66080.50780.57120.00190.297-0.57060.0279-0.23880.1063-0.0069-0.0868-0.16540.25830.0298-0.03450.18660.10360.475729.597593.2968101.5521
120.0854-0.00040.05880.01030.00310.05370.01240.1628-0.1929-0.7878-0.00210.22930.4852-0.41770.00060.4782-0.09250.01720.4728-0.0760.490619.737780.772150.2556
130.96690.4094-0.15120.5774-0.02740.55480.0143-0.44750.0882-0.08240.04780.1037-0.0335-0.16590.00030.29130.00410.0140.4538-0.02520.259826.658288.902960.3348
140.40030.17580.52960.35270.09310.49190.297-0.4269-0.52270.2201-0.03290.00660.1762-0.24840.02160.4919-0.1029-0.02440.53560.13930.548631.731371.284964.0255
150.01050.0077-0.01280.0005-0.0062-0.0036-0.2078-0.0025-0.0931-0.2713-0.3737-0.09580.11490.0947-0.00140.87550.0482-0.00070.70040.0550.789349.795863.130748.8678
161.3279-0.43520.42630.482-0.17461.32080.21220.2353-0.6512-0.50560.0644-0.53710.42720.09870.57070.5123-0.0253-0.02540.2518-0.11670.489233.705172.277247.4975
170.1665-0.08740.04360.0266-0.01810.06020.01440.1755-0.0761-0.51580.0173-0.0183-0.34930.0625-0.0030.5205-0.0260.04760.3066-0.08050.337531.838183.057740.5536
180.0226-0.0042-0.02270.0135-0.00950.0502-0.10460.0076-0.0990.04290.16350.0316-0.039-0.1951-0.00051.14740.02640.29781.53120.61031.097427.404462.946591.2607
190.1060.0605-0.04580.0567-0.00350.01070.0733-0.1606-0.1842-0.13560.16740.21430.0548-0.14250.07520.9953-0.4177-0.07970.96990.36450.791826.997959.605980.1548
200.164-0.2075-0.2790.68360.72811.14470.0673-0.9856-0.2044-0.17090.44640.5947-0.171-0.49030.34990.1929-0.1429-0.07630.96470.2520.414227.323178.292479.0434
210.3070.36670.22590.35450.23450.17790.0641-0.60310.01790.1071-0.0374-0.0285-0.11390.185600.3437-0.0514-0.00060.6209-0.08140.39855.011994.33565.9802
220.84170.1701-0.63370.5133-0.01980.58380.1696-0.9252-0.26470.0548-0.3495-0.19640.05520.4512-0.12380.42460.046-0.14120.77920.04420.543361.898585.158970.1475
230.4459-0.14740.14090.16280.00740.40130.0202-0.0152-0.27540.053-0.1495-0.2698-0.1138-0.0264-0.00240.26610.01820.00430.3267-0.07740.316862.090493.353652.5655
240.12660.06830.03950.0008-0.03360.10750.0073-0.1910.22710.1013-0.06230.11020.17610.0107-0.00020.2611-0.032-0.01030.4617-0.03940.329456.521697.543552.534
250.0558-0.0727-0.01190.1981-0.0098-0.0106-0.12510.43440.04290.3410.1222-0.6122-0.19130.16240.00230.3586-0.1002-0.0260.6669-0.08690.563380.360166.832296.2126
260.1618-0.03120.17020.4743-0.23590.2358-0.1820.2676-0.23390.04630.20590.1118-0.08240.20290.07510.3714-0.0094-0.0020.4014-0.14890.411572.678757.6115101.1466
270.01730.03230.02750.03960.05810.061-0.0599-0.21440.28410.12930.2452-0.0431-0.0204-0.38030.010.47750.213-0.1210.8892-0.24020.956986.925445.795898.7756
280.0144-0.0250.10170.05810.080.22750.0108-0.3646-0.27930.359-0.0837-0.0846-0.0789-0.04-00.51540.0396-0.0920.5224-0.08130.476273.464164.0542115.2237
29-0.00570.0011-0.00260.01210.02120.0327-0.16710.37680.07960.16260.09920.16250.0387-0.12050.00010.61620.0023-0.05010.4054-0.14550.657457.784777.3935112.4036
300.05180.0077-0.0686-0.00120.00030.02710.23520.1850.21710.6463-0.199-0.2517-0.43740.2991-0.00030.6657-0.029-0.12960.5269-0.07580.668671.460980.4773112.276
310.10540.0359-0.13040.1320.00470.11410.06540.38090.36220.1813-0.0210.0615-0.43220.25580.01420.4075-0.0439-0.07910.4498-0.0010.569263.110376.9353100.0307
320.08620.0959-0.09820.0808-0.09250.1053-0.1581-0.05870.5391-0.2537-0.40740.0077-0.5768-0.2572-0.0010.6154-0.0838-0.08560.516-0.01910.486364.979474.623494.9805
331.1991-0.2720.10280.1326-0.00230.04220.11730.678-0.37280.14690.0008-0.062-0.11380.42050.05360.472-0.11020.05850.6122-0.04650.272169.34265.526888.3406
340.59920.1752-0.25490.3137-0.04370.5011-0.0454-0.28370.14720.3204-0.2316-0.1727-0.2167-0.0297-1.03680.86090.0722-0.32220.5081-0.24380.456270.306977.3573129.6208
350.30660.17920.05470.0941-0.04480.2782-0.1740.0149-0.21680.13080.1262-0.16550.0747-0.1050.00010.46310.03160.01430.3378-0.06260.353246.010551.5121110.5976
361.5927-0.0756-0.42931.51580.38990.8707-0.0691-0.03330.22020.31820.07130.1003-0.1042-0.22380.27580.4780.03380.03480.3574-0.04240.335139.66462.712111.3833
370.101-0.0059-0.15250.08830.27060.5329-0.04510.112-0.171-0.1699-0.10450.1366-0.08790.0391-0.09010.3752-0.0293-0.01450.3497-0.1740.42138.686346.769795.8926
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 52 )
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 141 )
3X-RAY DIFFRACTION3chain 'A' and (resid 142 through 163 )
4X-RAY DIFFRACTION4chain 'A' and (resid 164 through 222 )
5X-RAY DIFFRACTION5chain 'A' and (resid 223 through 260 )
6X-RAY DIFFRACTION6chain 'A' and (resid 261 through 274 )
7X-RAY DIFFRACTION7chain 'B' and (resid 5 through 54 )
8X-RAY DIFFRACTION8chain 'B' and (resid 55 through 181 )
9X-RAY DIFFRACTION9chain 'B' and (resid 182 through 219 )
10X-RAY DIFFRACTION10chain 'B' and (resid 220 through 290 )
11X-RAY DIFFRACTION11chain 'B' and (resid 291 through 345 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 28 )
13X-RAY DIFFRACTION13chain 'C' and (resid 29 through 141 )
14X-RAY DIFFRACTION14chain 'C' and (resid 142 through 198 )
15X-RAY DIFFRACTION15chain 'C' and (resid 199 through 211 )
16X-RAY DIFFRACTION16chain 'C' and (resid 212 through 247 )
17X-RAY DIFFRACTION17chain 'C' and (resid 248 through 274 )
18X-RAY DIFFRACTION18chain 'D' and (resid 1 through 16 )
19X-RAY DIFFRACTION19chain 'D' and (resid 17 through 40 )
20X-RAY DIFFRACTION20chain 'D' and (resid 41 through 66 )
21X-RAY DIFFRACTION21chain 'D' and (resid 67 through 145 )
22X-RAY DIFFRACTION22chain 'D' and (resid 146 through 244 )
23X-RAY DIFFRACTION23chain 'D' and (resid 245 through 313 )
24X-RAY DIFFRACTION24chain 'D' and (resid 314 through 345 )
25X-RAY DIFFRACTION25chain 'E' and (resid 2 through 28 )
26X-RAY DIFFRACTION26chain 'E' and (resid 29 through 96 )
27X-RAY DIFFRACTION27chain 'E' and (resid 97 through 109 )
28X-RAY DIFFRACTION28chain 'E' and (resid 110 through 151 )
29X-RAY DIFFRACTION29chain 'E' and (resid 152 through 163 )
30X-RAY DIFFRACTION30chain 'E' and (resid 164 through 184 )
31X-RAY DIFFRACTION31chain 'E' and (resid 185 through 211 )
32X-RAY DIFFRACTION32chain 'E' and (resid 212 through 240 )
33X-RAY DIFFRACTION33chain 'E' and (resid 241 through 264 )
34X-RAY DIFFRACTION34chain 'F' and (resid 3 through 66 )
35X-RAY DIFFRACTION35chain 'F' and (resid 67 through 145 )
36X-RAY DIFFRACTION36chain 'F' and (resid 146 through 283 )
37X-RAY DIFFRACTION37chain 'F' and (resid 284 through 344 )

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