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- PDB-3av0: Crystal structure of Mre11-Rad50 bound to ATP S -

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Basic information

Entry
Database: PDB / ID: 3av0
TitleCrystal structure of Mre11-Rad50 bound to ATP S
Components(DNA double-strand break repair ...) x 2
KeywordsRECOMBINATION / DNA repair / Calcineurin-like phosphoesterase / ABC transporter ATPase domain-like / DNA double-strand break repair / HerA-NurA complex / Nbs1 in eukaryotes
Function / homology
Function and homology information


DNA exonuclease activity / DNA end binding / Y-form DNA binding / 3'-5' exonuclease activity / double-strand break repair / manganese ion binding / endonuclease activity / Hydrolases; Acting on ester bonds / DNA repair / ATP hydrolysis activity ...DNA exonuclease activity / DNA end binding / Y-form DNA binding / 3'-5' exonuclease activity / double-strand break repair / manganese ion binding / endonuclease activity / Hydrolases; Acting on ester bonds / DNA repair / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / identical protein binding
Similarity search - Function
Mre11, C-terminal domain-like / Double Stranded RNA Binding Domain - #600 / DNA double-strand break repair protein Mre11, archaea-type / DNA double-strand break repair Rad50 ATPase, archaeal type / Rad50 zinc hook motif / RAD50, zinc hook / Rad50 zinc-hook domain profile. / Helicase, Ruva Protein; domain 3 / Rad50/SbcC-type AAA domain / AAA domain ...Mre11, C-terminal domain-like / Double Stranded RNA Binding Domain - #600 / DNA double-strand break repair protein Mre11, archaea-type / DNA double-strand break repair Rad50 ATPase, archaeal type / Rad50 zinc hook motif / RAD50, zinc hook / Rad50 zinc-hook domain profile. / Helicase, Ruva Protein; domain 3 / Rad50/SbcC-type AAA domain / AAA domain / Mre11 nuclease, N-terminal metallophosphatase domain / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Double Stranded RNA Binding Domain / Helix non-globular / Special / 4-Layer Sandwich / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ISOPROPYL ALCOHOL / DNA double-strand break repair Rad50 ATPase / DNA double-strand break repair protein Mre11
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsLim, H.S. / Kim, J.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: Source and taxonomy / Category: entity_src_gen
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_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_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_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_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

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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 protein mre11
B: DNA double-strand break repair rad50 ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,95312
Polymers87,7612
Non-polymers1,19210
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-16 kcal/mol
Surface area35340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.958, 147.129, 175.907
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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DNA double-strand break repair ... , 2 types, 2 molecules AB

#1: Protein DNA double-strand break repair protein mre11


Mass: 45370.930 Da / Num. of mol.: 1 / Fragment: Nuclease domain (UNP RESIDUES 1-313)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: rad50, MJ1322 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q58719
#2: Protein DNA double-strand break repair rad50 ATPase / Rad50 ABC-ATPase


Mass: 42389.930 Da / Num. of mol.: 1 / 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

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Non-polymers , 6 types, 30 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 10 % PEG 3350, 0.1M ADA pH6.2, 0.1M Lithium sulfate, 2% iso-propanol, 5% Acetonitrile , 1mM ATP, 5mM magnessium chloride , VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 14, 2010
RadiationMonochromator: Si 4-channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 20290 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 3.1→3.15 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(Phenix.AuroMR)model building
PHENIX(phenix.refine: 1.6.3_473)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1II7, 3AUY

1ii7

3auy


Resolution: 3.1→29.318 Å / SU ML: 0.4 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2764 1961 9.66 %random
Rwork0.2144 ---
all0.2205 20837 --
obs0.2205 20290 97.37 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.401 Å2 / ksol: 0.291 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.9147 Å2-0 Å20 Å2
2---14.4584 Å2-0 Å2
3---16.3731 Å2
Refinement stepCycle: LAST / Resolution: 3.1→29.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6001 0 73 20 6094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116175
X-RAY DIFFRACTIONf_angle_d1.3988288
X-RAY DIFFRACTIONf_dihedral_angle_d21.2062399
X-RAY DIFFRACTIONf_chiral_restr0.081890
X-RAY DIFFRACTIONf_plane_restr0.0051054
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1001-3.21070.36941870.284164989
3.2107-3.33910.35571870.2691174295
3.3391-3.49090.36421960.253179997
3.4909-3.67460.2791940.2379182898
3.6746-3.90430.31151890.2262184598
3.9043-4.2050.28652020.2218182999
4.205-4.62660.27941930.1995187699
4.6266-5.29270.26062030.20541876100
5.2927-6.65540.30742020.21741901100
6.6554-29.31910.21642080.1904198499

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