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- PDB-3qf7: The Mre11:Rad50 complex forms an ATP dependent molecular clamp in... -

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Basic information

Entry
Database: PDB / ID: 3qf7
TitleThe Mre11:Rad50 complex forms an ATP dependent molecular clamp in DNA double-strand break repair
Components
  • Mre11
  • Rad50
KeywordsHYDROLASE / ABC-ATPase / ATPase / Mre11
Function / homology
Function and homology information


DNA exonuclease activity / 3'-5' exonuclease activity / double-strand break repair / endonuclease activity / DNA recombination / DNA replication / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding
Similarity search - Function
Helix hairpin bin / RAD50, zinc hook / Rad50 zinc-hook domain profile. / Nuclease SbcCD subunit D / SbcC/RAD50-like, Walker B motif / Rad50/SbcC-type AAA domain / AAA domain / Mre11 nuclease, N-terminal metallophosphatase domain / Helix hairpin bin domain superfamily / Calcineurin-like phosphoesterase domain, ApaH type ...Helix hairpin bin / RAD50, zinc hook / Rad50 zinc-hook domain profile. / Nuclease SbcCD subunit D / SbcC/RAD50-like, Walker B motif / Rad50/SbcC-type AAA domain / AAA domain / Mre11 nuclease, N-terminal metallophosphatase domain / Helix hairpin bin domain superfamily / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Helix Hairpins / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Nuclease SbcCD subunit D / Probable DNA double-strand break repair Rad50 ATPase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMoeckel, C. / Lammens, K.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: The Mre11:Rad50 Structure Shows an ATP-Dependent Molecular Clamp in DNA Double-Strand Break Repair.
Authors: Lammens, K. / Bemeleit, D.J. / Moeckel, C. / Clausing, E. / Schele, A. / Hartung, S. / Schiller, C.B. / Lucas, M. / Angermueller, C. / Soeding, J. / Straesser, K. / Hopfner, K.P.
History
DepositionJan 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Advisory / Data collection ...Advisory / Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen ...diffrn_detector / entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Item: _diffrn_detector.detector
Revision 1.3Feb 21, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_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_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: Rad50
B: Rad50
D: Mre11
C: Mre11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6838
Polymers94,6224
Non-polymers1,0614
Water8,773487
1
A: Rad50
C: Mre11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8414
Polymers47,3112
Non-polymers5312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-27 kcal/mol
Surface area18970 Å2
MethodPISA
2
B: Rad50
D: Mre11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8414
Polymers47,3112
Non-polymers5312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-28 kcal/mol
Surface area18770 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8840 Å2
ΔGint-54 kcal/mol
Surface area34820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.149, 68.400, 71.111
Angle α, β, γ (deg.)98.64, 111.14, 92.03
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Rad50 /


Mass: 41073.895 Da / Num. of mol.: 2
Fragment: nucleotide binding domain, UNP residues 1-190 and 686-852
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1X1
#2: Protein/peptide Mre11 /


Mass: 6237.057 Da / Num. of mol.: 2
Fragment: C-terminal helix-loop-helix motif, UNP residues 337-379
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1X0
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 487 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAINS A AND B HAVE RESIDUES 191-685 DELETED FROM THE SEQUENCE

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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: 2.32 Å3/Da / Density % sol: 46.95 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20 % PEG 2000MME, 0.2 M Trimethylamine N-oxide, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationMonochromator: diamond sagitally focusing Ge (220) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.9→45.63 Å / Num. all: 64744 / Num. obs: 64744 / % possible obs: 94.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→36.17 Å / SU ML: 0.2 / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1907 2006 3.1 %random
Rwork0.157 ---
obs0.1581 64738 96.71 %-
all-64744 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.933 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.9511 Å2-0.4367 Å21.2925 Å2
2--1.1534 Å2-1.2792 Å2
3----3.1045 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6314 0 64 487 6865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076657
X-RAY DIFFRACTIONf_angle_d1.0738979
X-RAY DIFFRACTIONf_dihedral_angle_d15.3022690
X-RAY DIFFRACTIONf_chiral_restr0.071005
X-RAY DIFFRACTIONf_plane_restr0.0041146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.22591310.17454397X-RAY DIFFRACTION96
1.9475-2.00020.20821510.15934440X-RAY DIFFRACTION96
2.0002-2.0590.18651360.15414489X-RAY DIFFRACTION96
2.059-2.12550.181520.15074484X-RAY DIFFRACTION96
2.1255-2.20140.17531360.14244458X-RAY DIFFRACTION97
2.2014-2.28960.18951440.15174483X-RAY DIFFRACTION97
2.2896-2.39370.24491370.15824477X-RAY DIFFRACTION97
2.3937-2.51990.21791510.16554516X-RAY DIFFRACTION97
2.5199-2.67770.21871460.16584495X-RAY DIFFRACTION97
2.6777-2.88440.21371410.16194549X-RAY DIFFRACTION97
2.8844-3.17450.16591440.15784488X-RAY DIFFRACTION98
3.1745-3.63350.17881430.14514550X-RAY DIFFRACTION98
3.6335-4.57640.1441470.13344544X-RAY DIFFRACTION98
4.5764-36.17660.19871470.17354362X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: -3.1384 Å / Origin y: -40.5207 Å / Origin z: 26.7541 Å
111213212223313233
T0.0854 Å2-0.0011 Å2-0.0026 Å2-0.0835 Å2-0.0109 Å2--0.0897 Å2
L0.1871 °2-0.0015 °2-0.0364 °2-0.1589 °2-0.0413 °2--0.1818 °2
S0.0207 Å °0.0041 Å °0.0117 Å °0.0028 Å °0.021 Å °-0.0122 Å °-0.005 Å °-0.0239 Å °-0 Å °
Refinement TLS groupSelection details: all

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