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- PDB-1ii8: Crystal structure of the P. furiosus Rad50 ATPase domain -

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Basic information

Entry
Database: PDB / ID: 1ii8
TitleCrystal structure of the P. furiosus Rad50 ATPase domain
Components(Rad50 ABC-ATPase) x 2
KeywordsREPLICATION / Rad50 / Mre11 / DNA double-strand break repair / ATP
Function / homology
Function and homology information


double-strand break repair / 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 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #70 / 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 / 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
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsHopfner, K.-P. / Karcher, A. / Craig, L. / Woo, T.T. / Carney, J.P. / Tainer, J.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2001
Title: Structural biochemistry and interaction architecture of the DNA double-strand break repair Mre11 nuclease and Rad50-ATPase.
Authors: Hopfner, K.P. / Karcher, A. / Craig, L. / Woo, T.T. / Carney, J.P. / Tainer, J.A.
History
DepositionApr 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Rad50 ABC-ATPase
B: Rad50 ABC-ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8434
Polymers42,6532
Non-polymers1902
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7460 Å2
ΔGint-62 kcal/mol
Surface area18960 Å2
MethodPISA
2
A: Rad50 ABC-ATPase
B: Rad50 ABC-ATPase
hetero molecules

A: Rad50 ABC-ATPase
B: Rad50 ABC-ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6878
Polymers85,3074
Non-polymers3804
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area18970 Å2
ΔGint-135 kcal/mol
Surface area33860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.531, 99.531, 116.407
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Rad50 ABC-ATPase


Mass: 22672.248 Da / Num. of mol.: 1 / Fragment: N-terminal fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: P58301
#2: Protein Rad50 ABC-ATPase


Mass: 19981.195 Da / Num. of mol.: 1 / Fragment: C-terminal fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: P58301
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 63 / 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: 3.9 Å3/Da / Density % sol: 68.47 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 100 mM Na-Acetate, 8% PEG 6K, 10 mM Ca-Acetate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
220 mMphosphate1drop
3200 mM1dropNaCl
40.1 mMEDTA1drop
55 %glycerol1drop
6100 mMsodium acetate1reservoir
78 %PEG60001reservoir
810 mMcalcium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 26, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 119376 / Num. obs: 119376 / % possible obs: 83 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 7.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 2 % / Rmerge(I) obs: 0.348 / % possible all: 47.3
Reflection
*PLUS
Num. obs: 13527 / Num. measured all: 119376
Reflection shell
*PLUS
% possible obs: 47.3 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F2T

1f2t


Resolution: 3.02→28.84 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1889335.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh&Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.294 604 5.1 %RANDOM
Rwork0.255 ---
all0.255 11823 --
obs0.255 11823 87.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.72 Å2 / ksol: 0.22 e/Å3
Displacement parametersBiso mean: 90.5 Å2
Baniso -1Baniso -2Baniso -3
1-33.31 Å223.67 Å20 Å2
2--33.31 Å20 Å2
3----66.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.56 Å
Luzzati d res low-5 Å
Luzzati sigma a1.18 Å1.07 Å
Refinement stepCycle: LAST / Resolution: 3.02→28.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3002 0 10 63 3075
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.412
X-RAY DIFFRACTIONc_scbond_it1.662
X-RAY DIFFRACTIONc_scangle_it2.832.5
LS refinement shellHighest resolution: 3.02 Å / Total num. of bins used: 6 /
Num. reflection% reflection
Rwork990 -
Rfree-5.1 %
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 90.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5

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