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- PDB-3qg5: The Mre11:Rad50 complex forms an ATP dependent molecular clamp in... -

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Basic information

Entry
Database: PDB / ID: 3qg5
TitleThe Mre11:Rad50 complex forms an ATP dependent molecular clamp in DNA double-strand break repair
Components
  • Mre11
  • rad50
KeywordsHYDROLASE / ABC ATPase / nuclease
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
DNA double-strand break repair nuclease / 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 ...DNA double-strand break repair nuclease / 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 / 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 / 4-Layer Sandwich / Helix Hairpins / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Nuclease SbcCD subunit D / Probable DNA double-strand break repair Rad50 ATPase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.4 Å
AuthorsLammens, 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 24, 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 / pdbx_unobs_or_zero_occ_residues / software
Item: _diffrn_detector.detector
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Mar 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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 / _struct_conn.pdbx_leaving_atom_flag / _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
C: Mre11
D: Mre11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,3576
Polymers171,1734
Non-polymers1842
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10450 Å2
ΔGint-69 kcal/mol
Surface area67650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.190, 187.000, 300.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 41261.473 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) / Gene: rad50, TM_1636 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1X1
#2: Protein Mre11 /


Mass: 44324.781 Da / Num. of mol.: 2 / Fragment: UNP residues 8-385
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3

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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: 4.31 Å3/Da / Density % sol: 71.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 9 % PEG-6000, 5% MPD, 0,1M HEPES, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9774 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 3.4→20 Å / Num. all: 40428 / Num. obs: 40428 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
SHARPphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.4→19.997 Å / SU ML: 0.5 / σ(F): 1.37 / Phase error: 29.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2952 2020 5 %
Rwork0.2584 --
obs0.2602 40423 98.84 %
all-40428 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.955 Å2 / ksol: 0.171 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.746 Å2-0 Å20 Å2
2---6.9595 Å20 Å2
3---6.3619 Å2
Refinement stepCycle: LAST / Resolution: 3.4→19.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11589 0 12 0 11601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01811807
X-RAY DIFFRACTIONf_angle_d0.87215856
X-RAY DIFFRACTIONf_dihedral_angle_d19.9427409
X-RAY DIFFRACTIONf_chiral_restr0.0471750
X-RAY DIFFRACTIONf_plane_restr0.0042041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4002-3.48480.38171320.33462676X-RAY DIFFRACTION98
3.4848-3.57850.33641510.30552701X-RAY DIFFRACTION100
3.5785-3.68320.331500.29772746X-RAY DIFFRACTION100
3.6832-3.80130.33271520.28312710X-RAY DIFFRACTION100
3.8013-3.93610.30851210.26972767X-RAY DIFFRACTION100
3.9361-4.09250.27181420.25782749X-RAY DIFFRACTION100
4.0925-4.2770.28441490.23282731X-RAY DIFFRACTION99
4.277-4.50.2681700.23132717X-RAY DIFFRACTION99
4.5-4.77840.26551380.21612763X-RAY DIFFRACTION99
4.7784-5.14150.25541270.21542766X-RAY DIFFRACTION99
5.1415-5.64830.28781470.23982764X-RAY DIFFRACTION99
5.6483-6.44160.34241460.26542717X-RAY DIFFRACTION97
6.4416-8.02750.30141560.2712763X-RAY DIFFRACTION98
8.0275-19.9970.26531390.26672833X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.34970.56231.84743.82631.24221.7880.0855-0.2923-0.1037-0.0339-0.03490.51530.095-0.2176-0.00010.2825-0.0678-0.03890.2249-0.04260.22633.9701-49.429667.2816
20.92810.16450.61652.15541.44831.2072-0.57470.37930.1652-1.38850.18930.7463-0.55260.3619-0.04781.1654-0.2727-0.51810.27450.07630.40749.148-30.026842.6257
33.77762.98480.52983.6899-0.07940.8804-0.1076-0.0805-0.13550.02770.0638-0.71390.16760.4366-0.00020.4637-0.0762-0.06130.2444-0.08040.347224.2049-32.026166.3984
41.47250.81441.04851.27780.28780.99670.1559-0.06240.8278-0.1999-0.33610.66320.1665-0.3818-0.49340.195-0.54490.01961.46320.1838-1.015489.078824.7561168.026
51.82850.68050.5522.51831.52671.23460.1867-0.1517-0.0313-0.255-0.1642-0.02970.0162-0.017200.2099-0.0129-0.19580.2138-0.07210.460239.594811.228692.541
61.10360.3710.24961.2971.10430.95940.1599-1.02250.82230.3387-0.50910.74150.60720.546900.72140.07250.05590.8695-0.31580.837625.116214.4098105.8249
71.03330.7404-0.69311.11430.43281.8168-0.00690.0165-0.0273-0.1542-0.45980.66180.3538-0.8806-0.00020.1723-0.0404-0.12670.7049-0.27320.783422.31849.026494.7252
81.04010.45670.37313.3192.0582.7285-0.09990.0039-0.3633-0.1344-0.02550.06520.44850.0127-0.25460.426-0.1179-0.14010.401-0.06270.466937.5291-16.321380.616
91.8845-0.7778-1.41510.3280.46571.2711-0.72390.07150.9816-0.2781-0.2947-0.0763-0.94710.092101.0537-0.0637-0.58610.38780.21041.42333.849-22.663851.8911
101.5282-0.2861.02050.0583-0.36862.90950.2057-0.57670.01430.1643-0.03870.38730.3277-0.17820.00010.3952-0.0502-0.12140.44910.08810.277252.359424.2441117.748
112.47150.7521-0.6250.396-0.53453.5733-0.08690.2297-0.33570.1406-0.2519-0.6210.21550.3924-00.32270.0136-0.09620.38050.04010.590466.118926.4856102.9978
121.48720.57870.26040.4536-0.83511.9020.0432-1.04690.07280.1061-0.4959-0.2263-0.28320.42060.00170.4746-0.0998-0.15110.99020.16860.331164.236621.7376132.8211
131.081-0.1625-0.62691.2068-0.1761.16860.25120.0695-0.6457-1.5237-0.45810.30120.1116-0.3695-0.02031.2162-0.7436-0.03840.9113-0.16010.763283.942542.4921159.9577
140.0148-0.0204-0.01560.03380.02660.0195-0.6960.2808-0.4991-0.4357-0.7395-0.0539-0.18-0.327502.20120.2114-1.26612.7767-0.59911.588795.394647.4166180.1502
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:126)
2X-RAY DIFFRACTION2(chain A and resid 127:708)
3X-RAY DIFFRACTION3(chain A and resid 709:850)
4X-RAY DIFFRACTION4(chain B and resid 1:850)
5X-RAY DIFFRACTION5(chain C and resid 7:116)
6X-RAY DIFFRACTION6(chain C and resid 117:159)
7X-RAY DIFFRACTION7(chain C and resid 160:259)
8X-RAY DIFFRACTION8(chain C and resid 260:335)
9X-RAY DIFFRACTION9(chain C and resid 336:385)
10X-RAY DIFFRACTION10(chain D and resid 7:85)
11X-RAY DIFFRACTION11(chain D and resid 86:216)
12X-RAY DIFFRACTION12(chain D and resid 217:329)
13X-RAY DIFFRACTION13(chain D and resid 330:371)
14X-RAY DIFFRACTION14(chain D and resid 372:385)

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