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- PDB-1us8: The Rad50 signature motif: essential to ATP binding and biologica... -

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Basic information

Entry
Database: PDB / ID: 1us8
TitleThe Rad50 signature motif: essential to ATP binding and biological function
Components(DNA DOUBLE-STRAND BREAK REPAIR RAD50 ATPASE) x 2
KeywordsDNA REPAIR / ABC ATPASE / SIGNATURE MOTIF
Function / homology
Function and homology information


double-strand break repair / ATP hydrolysis activity / zinc ion binding / ATP binding / identical protein binding
Similarity search - Function
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. / Rad50/SbcC-type AAA domain / AAA domain / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold ...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. / Rad50/SbcC-type AAA domain / AAA domain / 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
Similarity search - Component
Biological speciesPYROCOCCUS FURIOSUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMoncalian, G. / Lengsfeld, B. / Bhaskara, V. / Hopfner, K.P. / Karcher, A. / Alden, E. / Tainer, J.A. / Paull, T.T.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The Rad50 Signature Motif: Essential to ATP Binding and Biological Function
Authors: Moncalian, G. / Lengsfeld, B. / Bhaskara, V. / Hopfner, K.P. / Karcher, A. / Alden, E. / Tainer, J.A. / Paull, T.T.
History
DepositionNov 20, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)33,2602
Polymers33,2602
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.541, 67.851, 69.930
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


Mass: 16894.648 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS FURIOSUS (archaea) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P58301
#2: Protein DNA DOUBLE-STRAND BREAK REPAIR RAD50 ATPASE / RAD50


Mass: 16364.932 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 739-882 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS FURIOSUS (archaea) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P58301
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUES SER 793 ARG

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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: 2.43 Å3/Da / Density % sol: 48.94 %
Crystal growpH: 7.5
Details: 20 % PEG8000, 0.1 M MES PH 6.0, 0.2 M CALCIUM ACETATE
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14 mg/mlprotein1drop
220 mMTris-HCl1droppH7.0
3200 mM1dropNaCl
41 mMdithiothreitol1drop
50.5 mMEDTA1drop
62.5 mMATPgammaS1drop
710 mM1dropMgCl2
820 %(w/v)PEG80001reservoir
90.1 MMES1reservoirpH6.0
100.2 Mcalcium acetate1reservoir

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.849961
DetectorDate: Nov 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.849961 Å / Relative weight: 1
ReflectionResolution: 2.1→19.75 Å / Num. obs: 25989 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 10
Reflection shellResolution: 2.05→2.14 Å / Redundancy: 4 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 3 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Num. measured all: 200189 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 98.9 % / Rmerge(I) obs: 0.279

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F2T

1f2t


Resolution: 2.1→19.75 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 407016.46 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.219 910 4.9 %RANDOM
Rwork0.219 ---
obs0.219 18579 96.1 %-
Solvent computationSolvent model: FLAT MODEL / ksol: 0.381882 e/Å3
Displacement parametersBiso mean: 36 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å20 Å20 Å2
2--1.12 Å20 Å2
3---0.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2161 0 0 93 2254
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.61
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.671.5
X-RAY DIFFRACTIONc_mcangle_it2.612
X-RAY DIFFRACTIONc_scbond_it2.722
X-RAY DIFFRACTIONc_scangle_it4.272.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.218 141 4.8 %
Rwork0.224 2815 -
obs--93.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Num. reflection obs: 18606 / Num. reflection Rfree: 908 / % reflection Rfree: 5 % / Rfactor Rfree: 0.249 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.08
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.61

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