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- PDB-3qks: Mre11 Rad50 binding domain bound to Rad50 -

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Basic information

Entry
Database: PDB / ID: 3qks
TitleMre11 Rad50 binding domain bound to Rad50
Components
  • (DNA double-strand break repair rad50 ATPase) x 2
  • DNA double-strand break repair protein mre11
KeywordsREPLICATION / RecA-like fold / coiled-coils / ATPase / exonuclease / endonuclease / ATP binding / DNA binding
Function / homology
Function and homology information


DNA end binding / Y-form DNA binding / DNA double-strand break processing / 3'-5' exonuclease activity / DNA endonuclease activity / double-strand break repair / manganese ion binding / endonuclease activity / Hydrolases; Acting on ester bonds / ATP hydrolysis activity ...DNA end binding / Y-form DNA binding / DNA double-strand break processing / 3'-5' exonuclease activity / DNA endonuclease activity / double-strand break repair / manganese ion binding / endonuclease activity / Hydrolases; Acting on ester bonds / ATP hydrolysis activity / zinc ion binding / ATP binding / identical protein binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #70 / : / : / Mre11 nuclease, second domain / DNA double-strand break repair protein Mre11, archaea-type / DNA double-strand break repair Rad50 ATPase, archaeal type / AAA domain, putative AbiEii toxin, Type IV TA system / Rad50 zinc hook motif / RAD50, zinc hook / Rad50 zinc-hook domain profile. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #70 / : / : / Mre11 nuclease, second domain / DNA double-strand break repair protein Mre11, archaea-type / DNA double-strand break repair Rad50 ATPase, archaeal type / AAA domain, putative AbiEii toxin, Type IV TA system / Rad50 zinc hook motif / RAD50, zinc hook / Rad50 zinc-hook domain profile. / : / Mre11 nuclease, N-terminal metallophosphatase domain / Rad50/SbcC-type AAA domain / AAA domain / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA double-strand break repair Rad50 ATPase / DNA double-strand break repair protein Mre11
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWilliams, G.J. / Williams, R.S. / Arvai, A. / Moncalian, G. / Tainer, J.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: ABC ATPase signature helices in Rad50 link nucleotide state to Mre11 interface for DNA repair.
Authors: Williams, G.J. / Williams, R.S. / Williams, J.S. / Moncalian, G. / Arvai, A.S. / Limbo, O. / Guenther, G. / Sildas, S. / Hammel, M. / Russell, P. / Tainer, J.A.
History
DepositionFeb 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references / 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
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
B: DNA double-strand break repair rad50 ATPase
C: DNA double-strand break repair protein mre11


Theoretical massNumber of molelcules
Total (without water)48,2323
Polymers48,2323
Non-polymers00
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8320 Å2
ΔGint-63 kcal/mol
Surface area20370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.779, 91.232, 107.331
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 / Rad50 ABC-ATPase


Mass: 23615.232 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-195)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: rad50, PF1167 / Production host: Escherichia coli (E. coli)
References: UniProt: P58301, Hydrolases; Acting on acid anhydrides
#2: Protein DNA double-strand break repair rad50 ATPase / Rad50 ABC-ATPase


Mass: 20553.785 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 704-882)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: rad50, PF1167 / Production host: Escherichia coli (E. coli)
References: UniProt: P58301, Hydrolases; Acting on acid anhydrides
#3: Protein/peptide DNA double-strand break repair protein mre11 / Mre11 Nuclease / pfMre11


Mass: 4062.568 Da / Num. of mol.: 1 / Fragment: Rad50 binding domain (UNP residues 348-381)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: mre11, PF1166 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8U1N9, Hydrolases; Acting on ester bonds
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.86 Å3/Da / Density % sol: 57.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Tris, 200 mM magnesium chloride, 20% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2003
RadiationMonochromator: SINGLE CRYSTAL SI(111) BENT MONOCHOROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→38.67 Å / Num. all: 32699 / Num. obs: 31661 / % possible obs: 96.83 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 27.5
Reflection shellResolution: 2.1→2.1679 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 2.8 / % possible all: 86

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1II8

1ii8


Resolution: 2.1→38.67 Å / SU ML: 0.35 / σ(F): 1.33 / Phase error: 29.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2561 1602 5.06 %RANDOM
Rwork0.2101 ---
obs0.2125 31661 96.83 %-
all-32699 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 85.831 Å2 / ksol: 0.388 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.2998 Å2-0 Å20 Å2
2---0.5013 Å20 Å2
3---0.2014 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3237 0 0 244 3481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033283
X-RAY DIFFRACTIONf_angle_d0.6794402
X-RAY DIFFRACTIONf_dihedral_angle_d14.0471270
X-RAY DIFFRACTIONf_chiral_restr0.046501
X-RAY DIFFRACTIONf_plane_restr0.003552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.16790.36321130.29852394X-RAY DIFFRACTION86
2.1679-2.24530.29751210.25722594X-RAY DIFFRACTION93
2.2453-2.33520.33871640.25232715X-RAY DIFFRACTION98
2.3352-2.44150.33061480.24222736X-RAY DIFFRACTION99
2.4415-2.57020.26891360.23392798X-RAY DIFFRACTION99
2.5702-2.73120.30771500.22692762X-RAY DIFFRACTION99
2.7312-2.9420.27681390.22262825X-RAY DIFFRACTION100
2.942-3.23790.30861490.22722799X-RAY DIFFRACTION100
3.2379-3.70610.23251440.19612842X-RAY DIFFRACTION99
3.7061-4.6680.20251720.16692797X-RAY DIFFRACTION98
4.668-38.67940.23931660.20432797X-RAY DIFFRACTION94
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)
11.0476-1.5531-0.3091.49711.14542.7118-0.00220.0961-0.06350.1646-0.0550.32230.1125-0.24050.00020.3215-0.0050.02510.3861-0.04870.368325.303218.102634.4593
21.403-0.08580.34543.1161-0.17723.11330.08540.1703-0.1092-0.2728-0.0318-0.0470.5141-0.0198-0.00020.36380.00540.03690.3501-0.0860.339631.26889.165528.2744
30.39470.4379-0.08270.54530.08560.36780.0524-0.01210.233-0.10440.0040.68210.1771-0.81760.00050.4171-0.13390.00810.4917-0.03540.444621.49337.802755.9574
40.04540.17850.0240.29020.05030.0243-0.1580.3210.81621.1322-0.02740.0225-1.3073-0.2939-0.00961.6550.16460.01010.6553-0.10011.338731.0171-8.40449.47
52.6888-0.34952.17630.2286-0.21381.5418-0.1303-0.0438-0.30110.11280.07360.31520.2583-0.0463-0.00070.66330.00340.0780.35890.07790.472924.935-37.596341.9406
6-0.60760.31180.41590.6411-0.0720.57160.0166-0.01440.01780.9680.2408-0.40520.50850.1783-0.00040.4887-0.0343-0.01090.2609-0.06550.442532.4931-16.673656.064
73.30150.58590.12541.29560.10012.96940.1457-0.5320.0380.103-0.01410.01070.1993-0.29750.00010.3005-0.02150.0040.3826-0.00550.322229.273414.22162.7155
80.10250.29470.1890.32760.46640.2338-0.16411.06450.41250.71190.40540.1198-0.4736-0.29430.00230.530.0341-0.03520.391-0.04070.563722.579727.880258.0501
90.68950.25251.23250.8715-0.13721.22650.0303-0.80850.00230.56880.19550.0512-0.578-0.3978-0.00020.44480.03890.07920.4754-0.05470.389530.220127.143348.4569
100.15960.1374-0.2330.1002-0.11960.2666-0.41240.37420.4491-0.27480.25350.1097-0.9018-0.2465-0.00060.48480.1052-0.0110.50450.01110.495521.691730.630233.6556
110.3004-0.25920.03580.2594-0.05010.0497-0.1556-0.5888-0.11811.30781.4283-1.16670.0744-1.4171-0.00020.8653-0.10740.08530.8865-0.4191.547541.1886-18.832250.8579
120.05150.0821-0.04310.04970.00170.07350.17720.44311.1097-0.2394-0.0888-0.54870.1539-0.1064-0.00231.2973-0.20210.50860.651-0.09011.112737.0032-15.83443.9728
130.28860.13750.07820.17790.00750.0362-1.1431-0.23740.9519-0.0943-0.2184-1.2710.0631-1.1998-0.00260.77920.01850.04760.61120.00780.85434.3984-23.437640.9627
140.0315-0.04010.14630.3114-0.01870.4908-0.0235-0.5973-1.92670.3719-0.01430.33821.5094-0.1970.00460.79080.0398-0.08990.29210.11320.876138.4932-28.455445.3442
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:56)
2X-RAY DIFFRACTION2(chain A and resid 57:138)
3X-RAY DIFFRACTION3(chain A and resid 139:161)
4X-RAY DIFFRACTION4(chain A and resid 162:171)
5X-RAY DIFFRACTION5(chain A and resid 172:199) or (chain B and resid 704:713)
6X-RAY DIFFRACTION6(chain B and resid 714:750)
7X-RAY DIFFRACTION7(chain B and resid 751:826)
8X-RAY DIFFRACTION8(chain B and resid 827:840)
9X-RAY DIFFRACTION9(chain B and resid 841:864)
10X-RAY DIFFRACTION10(chain B and resid 865:882)
11X-RAY DIFFRACTION11(chain C and resid 353:358)
12X-RAY DIFFRACTION12(chain C and resid 359:369)
13X-RAY DIFFRACTION13(chain C and resid 370:374)
14X-RAY DIFFRACTION14(chain C and resid 375:379)

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