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- PDB-3auy: Crystal structure of Rad50 bound to ADP -

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Basic information

Entry
Database: PDB / ID: 3auy
TitleCrystal structure of Rad50 bound to ADP
ComponentsDNA double-strand break repair rad50 ATPase
KeywordsRECOMBINATION / DNA repair / ABC transporter ATPase domain-like / P-loop containing nucleoside triphosphate hydrolases / Mre11
Function / homology
Function and homology information


double-strand break repair / ATP hydrolysis activity / zinc ion binding / ATP binding
Similarity search - Function
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 / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold ...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 / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DNA double-strand break repair Rad50 ATPase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLim, H.S. / Cho, Y.
CitationJournal: To be Published
Title: Crystal Structure of the Mre11-Rad50-ATP S Complex: Understanding the Interplay between Mre11 and Rad50
Authors: Lim, H.S. / Kim, J.S. / Park, Y.B. / Gwon, G.H. / Cho, Y.
History
DepositionFeb 18, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 1, 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 / 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_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.ptnr1_label_seq_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.ptnr3_label_seq_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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)85,6836
Polymers84,7802
Non-polymers9034
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-23 kcal/mol
Surface area33490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.160, 95.300, 110.980
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


Mass: 42389.930 Da / Num. of mol.: 2 / Fragment: ABC ATPase domain (UNP RESIDUES 1-190, 825-1005)
Source method: isolated from a genetically manipulated source
Details: The fusion protein of residues 1-190 and residues 825-1005
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: rad50, MJ1322 / Production host: Escherichia coli (E. coli) / References: UniProt: Q58718
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 9.5% PEG 8000, 0.1M sodium cacodylate pH6.5, 0.1M magnessium acetate, 1mM ADP, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 12, 2010
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.63→72.3 Å / Num. all: 25069 / Num. obs: 24959 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 27 Å2
Reflection shellResolution: 2.63→2.72 Å / % possible all: 99.1

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ii8

1ii8


Resolution: 2.7→19.4 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 299173.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: deviations from ideal value / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.296 2287 9.9 %RANDOM
Rwork0.228 ---
obs0.228 23077 99 %-
all-23322 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.0384 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 55.1 Å2
Baniso -1Baniso -2Baniso -3
1-9.22 Å20 Å20 Å2
2---1.64 Å20 Å2
3----7.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5807 0 56 69 5932
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.272
X-RAY DIFFRACTIONc_scbond_it1.752
X-RAY DIFFRACTIONc_scangle_it2.822.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.358 370 9.8 %
Rwork0.293 3416 -
obs--99.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2adp.paramadp.top
X-RAY DIFFRACTION3ion.paramwater.top
X-RAY DIFFRACTION4water_rep.paramion.top

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