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- PDB-3thn: Crystal structure of Mre11 core with manganese -

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Basic information

Entry
Database: PDB / ID: 3thn
TitleCrystal structure of Mre11 core with manganese
ComponentsExonuclease, putative
KeywordsHYDROLASE / DNA breaks / homologous recombination / DNA binding Protein / Endodeoxyribonucleases / Exodeoxyribonucleases
Function / homology
Function and homology information


DNA exonuclease activity / 3'-5' exonuclease activity / DNA endonuclease activity / double-strand break repair / DNA recombination / DNA replication / Hydrolases; Acting on ester bonds / DNA repair / DNA binding / metal ion binding
Similarity search - Function
DNA double-strand break repair nuclease / Nuclease SbcCD subunit D / 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 / 4-Layer Sandwich ...DNA double-strand break repair nuclease / Nuclease SbcCD subunit D / 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 / 4-Layer Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / DNA double-strand break repair protein Mre11
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.811 Å
AuthorsMoeckel, C. / Lammens, K.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: ATP driven structural changes of the bacterial Mre11:Rad50 catalytic head complex.
Authors: Mockel, C. / Lammens, K. / Schele, A. / Hopfner, K.P.
History
DepositionAug 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Feb 28, 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: Exonuclease, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9196
Polymers36,5211
Non-polymers3985
Water21612
1
A: Exonuclease, putative
hetero molecules

A: Exonuclease, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,83812
Polymers73,0422
Non-polymers79610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area6400 Å2
ΔGint-139 kcal/mol
Surface area26460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.859, 138.859, 123.102
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-3-

SO4

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Components

#1: Protein Exonuclease, putative /


Mass: 36520.875 Da / Num. of mol.: 1 / Fragment: core domain, UNP residues 7-325 / Mutation: H94Q, F291S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: Mre11, TM_1635 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1X0
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 1

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Sample preparation

CrystalDensity Matthews: 4.69 Å3/Da / Density % sol: 73.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Sodium sulfate, 0.1M Bis Tris propane, pH 6.5, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8109→46.058 Å / Num. all: 17628 / Num. obs: 17314 / Observed criterion σ(I): 17.82

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.811→46.058 Å / SU ML: 0.74 / σ(F): 2 / Phase error: 21.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2406 1731 10 %
Rwork0.1869 --
obs0.1921 17309 98.43 %
all-17309 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 18.596 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.9676 Å2-0 Å20 Å2
2---2.9676 Å20 Å2
3---5.9351 Å2
Refinement stepCycle: LAST / Resolution: 2.811→46.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2531 0 17 12 2560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082600
X-RAY DIFFRACTIONf_angle_d1.233500
X-RAY DIFFRACTIONf_dihedral_angle_d17.83989
X-RAY DIFFRACTIONf_chiral_restr0.091385
X-RAY DIFFRACTIONf_plane_restr0.005449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8109-2.89360.34191400.28381268X-RAY DIFFRACTION97
2.8936-2.9870.32141410.25571257X-RAY DIFFRACTION100
2.987-3.09370.32441430.23171290X-RAY DIFFRACTION99
3.0937-3.21750.28731420.21991278X-RAY DIFFRACTION100
3.2175-3.36390.2921430.20431285X-RAY DIFFRACTION99
3.3639-3.54120.24241410.21331273X-RAY DIFFRACTION99
3.5412-3.7630.23021440.18321298X-RAY DIFFRACTION99
3.763-4.05340.21921430.15641292X-RAY DIFFRACTION99
4.0534-4.4610.18311450.14371296X-RAY DIFFRACTION98
4.461-5.10580.16961450.13121310X-RAY DIFFRACTION98
5.1058-6.430.23751490.18251332X-RAY DIFFRACTION98
6.43-46.0640.24431550.19841399X-RAY DIFFRACTION96

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