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- PDB-1l8d: Rad50 coiled-coil Zn hook -

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Basic information

Entry
Database: PDB / ID: 1l8d
TitleRad50 coiled-coil Zn hook
ComponentsDNA double-strand break repair rad50 ATPase
KeywordsREPLICATION / zinc finger / rad50 / DNA repair / Recombination / hook 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
Helix hairpin bin / 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 / ATPase, AAA-type, core / Helix Hairpins ...Helix hairpin bin / 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 / ATPase, AAA-type, core / Helix Hairpins / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRIC ACID / : / PHOSPHATE ION / DNA double-strand break repair Rad50 ATPase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsHopfner, K.P. / Tainer, J.A.
CitationJournal: Nature / Year: 2002
Title: The Rad50 zinc-hook is a structure joining Mre11 complexes in DNA recombination and repair.
Authors: Hopfner, K.P. / Craig, L. / Moncalian, G. / Zinkel, R.A. / Usui, T. / Owen, B.A. / Karcher, A. / Henderson, B. / Bodmer, J.L. / McMurray, C.T. / Carney, J.P. / Petrini, J.H. / Tainer, J.A.
History
DepositionMar 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,26910
Polymers26,3072
Non-polymers9638
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-53 kcal/mol
Surface area14540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.958, 77.868, 53.330
Angle α, β, γ (deg.)90, 91.55, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA double-strand break repair rad50 ATPase


Mass: 13153.300 Da / Num. of mol.: 2
Fragment: Rad50 coiled-coil fragment containing the CXXC motif, Rad50 molecular hook
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: P58301
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.52 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 100 mM Phosphate/Citrate, 40% Ethanol, 50 mM Zn-Acetate, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130 mg/mlprotein1drop
220 mMphosphate1droppH7.5
3200 mM1dropNaCl
40.1 mMEDTA1drop
55 %glycerol1drop
62 mMdithiothreitol1drop
7100 mMphosphate/citrate1reservoirpH4.2
840 %ethanol1reservoir
910 %glycerol1reservoir
1020 mMzinc acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.8321, 1.009
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.83211
21.0091
ReflectionResolution: 2.2→30 Å / Num. obs: 13119 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.2→2.25 Å / % possible all: 62.9
Reflection
*PLUS
% possible obs: 88 % / Num. measured all: 133282 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 62.9 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
MLPHAREphasing
CNSrefinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.278 548 random
Rwork0.225 --
obs-10580 -
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1689 0 44 124 1857
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.79
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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