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- PDB-4yke: Crystal structure of eukaryotic Mre11 catalytic domain from Chaet... -

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Basic information

Entry
Database: PDB / ID: 4yke
TitleCrystal structure of eukaryotic Mre11 catalytic domain from Chaetomium thermophilum
ComponentsMre11
KeywordsHYDROLASE / nuclease / Catalytic Domain / Nuclear Proteins / Protein Binding
Function / homology
Function and homology information


Mre11 complex / 3'-5'-DNA exonuclease activity / DNA endonuclease activity / meiotic cell cycle / double-strand break repair / manganese ion binding
Similarity search - Function
Mre11, capping domain / DNA double-strand break repair protein Mre11 / Mre11, DNA-binding / Mre11, capping domain / Mre11 DNA-binding presumed domain / Mre11 DNA-binding presumed domain / Mre11 nuclease, N-terminal metallophosphatase domain / Translation Initiation Factor IF3 / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 ...Mre11, capping domain / DNA double-strand break repair protein Mre11 / Mre11, DNA-binding / Mre11, capping domain / Mre11 DNA-binding presumed domain / Mre11 DNA-binding presumed domain / Mre11 nuclease, N-terminal metallophosphatase domain / Translation Initiation Factor IF3 / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Double-strand break repair protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.783 Å
AuthorsSeifert, F.U. / Lammens, K. / Hopfner, K.-P.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structure of the catalytic domain of Mre11 from Chaetomium thermophilum.
Authors: Seifert, F.U. / Lammens, K. / Hopfner, K.P.
History
DepositionMar 4, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mre11
B: Mre11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,1886
Polymers125,9682
Non-polymers2204
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-38 kcal/mol
Surface area37720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.722, 56.555, 304.562
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 Mre11 /


Mass: 62984.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0007600 / Production host: Escherichia coli (E. coli) / References: UniProt: G0RYR3
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.57 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: Ammonium citrate tribasic, PEG3350 / PH range: 6.8 - 7.0

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Data collection

DiffractionMean temperature: 199.4 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9796 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.78→50 Å / Num. obs: 25153 / % possible obs: 98.1 % / Redundancy: 6.7 % / Rsym value: 0.125 / Net I/σ(I): 11.18
Reflection shellResolution: 2.78→2.95 Å / Redundancy: 6.13 % / Rmerge(I) obs: 0.884 / Mean I/σ(I) obs: 1.81 / % possible all: 89.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
PHASERphasing
Cootmodel building
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FBQ

4fbq


Resolution: 2.783→49.517 Å / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.51 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2312 1251 4.97 %
Rwork0.198 --
obs0.2015 25153 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.783→49.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6548 0 4 60 6612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036703
X-RAY DIFFRACTIONf_angle_d0.6839067
X-RAY DIFFRACTIONf_dihedral_angle_d11.9872553
X-RAY DIFFRACTIONf_chiral_restr0.029977
X-RAY DIFFRACTIONf_plane_restr0.0031194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7833-2.89470.40141100.30832253X-RAY DIFFRACTION81
2.8947-3.02650.26071390.26112648X-RAY DIFFRACTION95
3.0265-3.1860.26361300.24352676X-RAY DIFFRACTION95
3.186-3.38550.27111340.22742653X-RAY DIFFRACTION95
3.3855-3.64670.23031510.21312671X-RAY DIFFRACTION95
3.6467-4.01350.24781340.19832703X-RAY DIFFRACTION95
4.0135-4.59360.20421440.17762667X-RAY DIFFRACTION95
4.5936-5.78490.2011470.16822762X-RAY DIFFRACTION95
5.7849-41.51550.21371560.19042873X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: -24.9959 Å / Origin y: 18.2406 Å / Origin z: -37.7695 Å
111213212223313233
T0.2193 Å20.0693 Å2-0.1074 Å2-0.1901 Å2-0.042 Å2--0.1136 Å2
L0.6101 °2-0.0559 °20.0884 °2-0.4534 °2-0.0747 °2--0.2583 °2
S0.0334 Å °0.0021 Å °0.001 Å °0.0389 Å °0.0509 Å °0.0683 Å °0.0449 Å °-0.0031 Å °0.0254 Å °
Refinement TLS groupSelection details: all

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