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- PDB-1f2t: Crystal Structure of ATP-Free RAD50 ABC-ATPase -

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Basic information

Entry
Database: PDB / ID: 1f2t
TitleCrystal Structure of ATP-Free RAD50 ABC-ATPase
Components(RAD50 ABC-ATPASE) x 2
KeywordsREPLICATION / DNA double-strand break repair / ABC ATPase
Function / homologyDNA double-strand break repair Rad50 ATPase, archaeal type / P-loop containing nucleoside triphosphate hydrolase / Rad50 zinc-hook domain profile. / AAA domain / AAA domain, putative AbiEii toxin, Type IV TA system / Rad50 zinc hook motif / ATPase, AAA-type, core / RAD50, zinc hook / Rad50/SbcC-type AAA domain / SbcC-like ...DNA double-strand break repair Rad50 ATPase, archaeal type / P-loop containing nucleoside triphosphate hydrolase / Rad50 zinc-hook domain profile. / AAA domain / AAA domain, putative AbiEii toxin, Type IV TA system / Rad50 zinc hook motif / ATPase, AAA-type, core / RAD50, zinc hook / Rad50/SbcC-type AAA domain / SbcC-like / nuclease activity / double-strand break repair / ATPase activity / zinc ion binding / ATP binding / identical protein binding / DNA double-strand break repair Rad50 ATPase
Function and homology information
Specimen sourcePyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 1.6 Å resolution
AuthorsHopfner, K.P. / Karcher, A. / Shin, D.S. / Craig, L.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: Structural biology of Rad50 ATPase: ATP-driven conformational control in DNA double-strand break repair and the ABC-ATPase superfamily.
Authors: Hopfner, K.P. / Karcher, A. / Shin, D.S. / Craig, L. / Arthur, L.M. / Carney, J.P. / Tainer, J.A.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 29, 2000 / Release: Aug 2, 2000
RevisionDateData content typeGroupProviderType
1.0Aug 2, 2000Structure modelrepositoryInitial release
1.1Oct 21, 2007Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance

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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


Theoretical massNumber of molelcules
Total (without water)33,8982
Polyers33,8982
Non-polymers00
Water7,548419
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)4510
ΔGint (kcal/M)-25
Surface area (Å2)14320
MethodPISA,PQS
Unit cell
γ
α
β
Length a, b, c (Å)66.57, 67.08, 70.06
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP 21 21 21

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Components

#1: Protein/peptide RAD50 ABC-ATPASE


Mass: 17110.840 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN / Source: (gene. exp.) Pyrococcus furiosus (archaea) / Genus: Pyrococcus / Plasmid name: PET29 / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P58301
#2: Protein/peptide RAD50 ABC-ATPASE


Mass: 16787.430 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN / Source: (gene. exp.) Pyrococcus furiosus (archaea) / Genus: Pyrococcus / Plasmid name: PET29 / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P58301
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / Formula: H2O / Water

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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: 2.31 / Density percent sol: 46.68 %
Crystal growTemp: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200 mM ammonium acetate, 50 mM cacodylate, 10 mM MgCl2, 10% PEG 4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal grow
*PLUS
pH: 6.8
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
18 mg/mlprotein1drop
220 mMNa-phosphate1drop
3300 mM1dropNaCl
41 mMEDTA1drop
5200 mMammonium acetate1reservoir
650 mMcacodylate1reservoir
710 mM1reservoirMgCl2
810 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Collection date: Nov 7, 1999
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 22.6 Å2 / D resolution high: 1.6 Å / D resolution low: 3 Å / Number all: 567133 / Number obs: 567133 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.055 / NetI over sigmaI: 12.6 / Redundancy: 4 % / Percent possible obs: 98.6
Reflection shellRmerge I obs: 0.366 / Highest resolution: 1.6 Å / Lowest resolution: 1.64 Å / Redundancy: 3.1 % / Percent possible all: 98.6
Reflection
*PLUS
Number obs: 46541
Reflection shell
*PLUS
Percent possible obs: 98.6

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
RefineR Free selection details: random 5% / Sigma F: 0 / Sigma I: 0 / Stereochemistry target values: Engh & Huber
Least-squares processR factor R free: 0.231 / R factor R work: 0.187 / R factor all: 0.187 / R factor obs: 0.187 / Highest resolution: 1.6 Å / Lowest resolution: 2 Å / Number reflection R free: 2034 / Number reflection all: 40425 / Number reflection obs: 38391 / Percent reflection obs: 98.6
Refine hist #LASTHighest resolution: 1.6 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 2310 / Nucleic acid: 0 / Ligand: 0 / Solvent: 419 / Total: 2729
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_bond_d0.010

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