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- PDB-1f2u: Crystal Structure of RAD50 ABC-ATPase -

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Basic information

Entry
Database: PDB / ID: 1f2u
TitleCrystal Structure of RAD50 ABC-ATPase
Components(RAD50 ABC-ATPASE) x 2
KeywordsREPLICATION / DNA double-strand break repair / ABC-ATPase
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
ADENOSINE-5'-TRIPHOSPHATE / DNA double-strand break repair Rad50 ATPase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
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.
History
DepositionMay 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: RAD50 ABC-ATPASE
B: RAD50 ABC-ATPASE
C: RAD50 ABC-ATPASE
D: RAD50 ABC-ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8608
Polymers67,7974
Non-polymers1,0634
Water6,720373
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.9, 82.6, 106.0
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RAD50 ABC-ATPASE


Mass: 17110.840 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: PET29 / Production host: Escherichia coli (E. coli) / References: UniProt: P58301
#2: Protein RAD50 ABC-ATPASE


Mass: 16787.430 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: PET29 / Production host: Escherichia coli (E. coli) / References: UniProt: P58301
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.58 Å3/Da / Density % sol: 52.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 17% PEG 3350, 8.5% isopropanol, 15% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.5 mMATP1drop
22.5 mMAMP-PNP1drop
310 mM1dropMgCl2
40.1 MHEPES1reservoir
517 %PEG33501reservoir
68.5 %isopropanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 26, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 444072 / Num. obs: 444072 / % possible obs: 81.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 11.6
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.302 / % possible all: 51.8
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 41804 / Num. measured all: 444072
Reflection shell
*PLUS
% possible obs: 51.8 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
RefinementResolution: 1.6→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh&Huber
RfactorNum. reflectionSelection details
Rfree0.282 1169 random 5%
Rwork0.238 --
all0.238 22902 -
obs0.238 21733 -
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4691 0 64 373 5128
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_bond_d0.01
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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