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

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Basic information

Entry
Database: PDB / ID: 3qkr
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 exonuclease 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 ...DNA exonuclease 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 / DNA double-strand break repair protein Mre11, archaea-type / 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 / Mre11 nuclease, N-terminal metallophosphatase domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #70 / DNA double-strand break repair protein Mre11, archaea-type / 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 / Mre11 nuclease, N-terminal metallophosphatase 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 / ATPase, AAA-type, core / Special / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / 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: 3.4 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 ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4225
Polymers48,2323
Non-polymers1902
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9250 Å2
ΔGint-76 kcal/mol
Surface area21110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.041, 116.041, 109.853
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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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: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 4.48 Å3/Da / Density % sol: 72.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris, 200-300 mM lithium sulfate, 12-13% PEG3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97591
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: 0.97591 Å / Relative weight: 1
ReflectionResolution: 3.4→100 Å / Num. all: 11608 / Num. obs: 10679 / % possible obs: 91.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 14.2
Reflection shellResolution: 3.4→3.488 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 2 / % possible all: 56.39

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1II8

1ii8


Resolution: 3.4→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.871 / SU B: 22.309 / SU ML: 0.375 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.563 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27444 514 4.8 %RANDOM
Rwork0.21129 ---
obs0.21432 10142 91.63 %-
all-11648 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 99.954 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å2-0.37 Å20 Å2
2---0.73 Å20 Å2
3---1.1 Å2
Refinement stepCycle: LAST / Resolution: 3.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3339 0 10 7 3356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223412
X-RAY DIFFRACTIONr_angle_refined_deg1.0311.9834577
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3435410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.30623.899159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.62115683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6471527
X-RAY DIFFRACTIONr_chiral_restr0.0690.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022476
X-RAY DIFFRACTIONr_nbd_refined0.230.21729
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22339
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2129
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2490.26
X-RAY DIFFRACTIONr_mcbond_it19.8481.52100
X-RAY DIFFRACTIONr_mcangle_it26.93723302
X-RAY DIFFRACTIONr_scbond_it40.05531449
X-RAY DIFFRACTIONr_scangle_it50.8884.51275
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 24 -
Rwork0.266 457 -
obs--56.39 %

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