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- PDB-4nci: Crystal Structure of Pyrococcus furiosis Rad50 R805E mutation -

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Basic information

Entry
Database: PDB / ID: 4nci
TitleCrystal Structure of Pyrococcus furiosis Rad50 R805E mutation
ComponentsDNA double-strand break repair Rad50 ATPase
KeywordsDNA BINDING PROTEIN / Adenosine Triphosphatase / DNA Repair / Fungal Protein
Function / homology
Function and homology information


double-strand break repair / ATP hydrolysis activity / zinc ion binding / ATP binding / identical protein binding
Similarity search - Function
AAA domain, putative AbiEii toxin, Type IV TA system / DNA double-strand break repair Rad50 ATPase, archaeal type / Rad50 zinc hook motif / RAD50, zinc hook / Rad50 zinc-hook domain profile. / Rad50/SbcC-type AAA domain / AAA domain / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...AAA domain, putative AbiEii toxin, Type IV TA system / DNA double-strand break repair Rad50 ATPase, archaeal type / Rad50 zinc hook motif / RAD50, zinc hook / Rad50 zinc-hook domain profile. / Rad50/SbcC-type AAA domain / AAA domain / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA double-strand break repair Rad50 ATPase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsClassen, S. / Williams, G.J. / Arvai, A.S. / Williams, R.S.
CitationJournal: Embo J. / Year: 2014
Title: ATP-driven Rad50 conformations regulate DNA tethering, end resection, and ATM checkpoint signaling.
Authors: Deshpande, R.A. / Williams, G.J. / Limbo, O. / Williams, R.S. / Kuhnlein, J. / Lee, J.H. / Classen, S. / Guenther, G. / Russell, P. / Tainer, J.A. / Paull, T.T.
History
DepositionOct 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA double-strand break repair Rad50 ATPase


Theoretical massNumber of molelcules
Total (without water)38,5811
Polymers38,5811
Non-polymers00
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.108, 68.019, 74.487
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 DNA double-strand break repair Rad50 ATPase


Mass: 38580.535 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-177 AND 726-882 / Mutation: R805E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF1167, rad50 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: P58301
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: 100 mM Bicine, 6-14% PEG 20000, 2 mM Dioxane, pH 8.6, vapor diffusion, sitting drop, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
2901
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-110.97945
SYNCHROTRONALS 12.3.121.11583
Detector
TypeIDDetector
MARMOSAIC 325 mm CCD1CCD
MARMOSAIC 325 mm CCD2CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 DOUBLE CRYSTALSINGLE WAVELENGTHMx-ray1
2Si 111 DOUBLE CRYSTALSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979451
21.115831
ReflectionResolution: 2.3→50 Å / Num. obs: 30041 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 56.02 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.75
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.3-2.360.9141.611,299.8
2.36-2.430.7092.121,2100
2.43-2.50.4863.051,299.8
2.5-2.570.3933.731,2100
2.57-2.660.2974.941,2100
2.66-2.750.2096.921,299.9
2.75-2.850.1648.561,2100
2.85-2.970.1211.561,2100
2.97-3.10.09114.781,299.9
3.1-3.250.0718.061,2100
3.25-3.430.04725.121,2100
3.43-3.640.03431.791,299.9
3.64-3.890.02936.711,2100
3.89-4.20.02541.991,2100
4.2-4.60.02546.51,2100
4.6-5.150.02547.751,2100
5.15-5.940.02847.261,2100
5.94-7.280.02647.111,2100
7.28-10.290.01851.641,299.7
10.290.01752.991,291.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
PHENIXdev_1233refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→37.243 Å / Occupancy max: 1 / Occupancy min: 0.21 / SU ML: 0.34 / σ(F): 1.31 / Phase error: 25.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2583 1518 5.05 %
Rwork0.2015 --
obs0.2041 30041 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.1298 Å2
Refinement stepCycle: LAST / Resolution: 2.3→37.243 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 0 172 2548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032439
X-RAY DIFFRACTIONf_angle_d0.7263310
X-RAY DIFFRACTIONf_dihedral_angle_d12.644895
X-RAY DIFFRACTIONf_chiral_restr0.043393
X-RAY DIFFRACTIONf_plane_restr0.002421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.37410.31281260.30092546X-RAY DIFFRACTION98
2.3741-2.45890.31591500.28432580X-RAY DIFFRACTION100
2.4589-2.55730.29391590.27012578X-RAY DIFFRACTION100
2.5573-2.67370.25821370.24632613X-RAY DIFFRACTION100
2.6737-2.81460.31071730.22842564X-RAY DIFFRACTION100
2.8146-2.99090.34041250.23242630X-RAY DIFFRACTION100
2.9909-3.22170.2831250.22852595X-RAY DIFFRACTION100
3.2217-3.54570.25361500.20412594X-RAY DIFFRACTION100
3.5457-4.05820.21181340.17992617X-RAY DIFFRACTION100
4.0582-5.11080.20091050.16642630X-RAY DIFFRACTION100
5.1108-37.24840.28321340.19312576X-RAY DIFFRACTION99
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)
17.23123.5528-0.09414.8802-0.48155.5495-0.01850.10970.1342-0.0397-0.02170.4240.52-0.47430.13250.3810.0059-0.06140.3299-0.03720.4581-7.5754-6.145315.1333
26.62722.43853.72683.15160.25935.1158-0.14160.4250.3246-0.14740.13660.3251-0.18190.1748-0.00130.538-0.01840.01150.4088-0.04390.4243-0.43851.343311.2648
37.7674-0.11633.79423.13741.43195.58080.2268-0.5406-0.30670.2641-0.2368-0.44260.26680.22360.04250.4726-0.0991-0.02090.43320.07110.393518.67833.060529.8457
45.52683.183.30187.24432.93696.05850.5148-1.296-0.16381.182-0.2194-0.2070.4933-0.1159-0.2180.7275-0.07840.11260.7753-0.13520.5138-4.6918-6.956931.5593
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:59)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 67:165)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 730:822)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 823:882)

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