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- PDB-3auz: Crystal structure of Mre11 with manganese -

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Basic information

Entry
Database: PDB / ID: 3auz
TitleCrystal structure of Mre11 with manganese
ComponentsDNA double-strand break repair protein mre11
KeywordsRECOMBINATION / DNA repair / Calcineurin-like phosphoesterase / DNA double-strand break repair nuclease / Rad50
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 / DNA binding / identical protein binding
Similarity search - Function
Double Stranded RNA Binding Domain - #600 / DNA double-strand break repair protein Mre11, archaea-type / 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 ...Double Stranded RNA Binding Domain - #600 / DNA double-strand break repair protein Mre11, archaea-type / 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 speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.206 Å
AuthorsPark, Y.B. / 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 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
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_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: DNA double-strand break repair protein mre11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3654
Polymers39,1631
Non-polymers2023
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.980, 101.980, 113.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 39163.008 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: MJ1323, mre11 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q58719
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / 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: 5

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Sample preparation

CrystalDensity Matthews: 3.75 Å3/Da / Density % sol: 67.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 60% Tacsimate pH 7.0, 0.5mM manganese chloride , VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 10, 2010
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 10307 / Num. obs: 10290 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.2→3.31 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AV0

3av0


Resolution: 3.206→29.045 Å / SU ML: 0.45 / σ(F): 0.07 / Phase error: 26.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2625 985 9.98 %random
Rwork0.2192 ---
obs0.2235 9873 96.28 %-
all-10254 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 72.262 Å2 / ksol: 0.346 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.3425 Å20 Å20 Å2
2---3.3425 Å2-0 Å2
3---6.6851 Å2
Refinement stepCycle: LAST / Resolution: 3.206→29.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2627 0 8 0 2635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092697
X-RAY DIFFRACTIONf_angle_d1.253619
X-RAY DIFFRACTIONf_dihedral_angle_d21.2021028
X-RAY DIFFRACTIONf_chiral_restr0.075379
X-RAY DIFFRACTIONf_plane_restr0.005463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2062-3.3750.37651280.31431151X-RAY DIFFRACTION90
3.375-3.58610.32181330.27581214X-RAY DIFFRACTION94
3.5861-3.86240.27651370.2281237X-RAY DIFFRACTION96
3.8624-4.250.23321410.20081277X-RAY DIFFRACTION97
4.25-4.86240.27341450.1881295X-RAY DIFFRACTION98
4.8624-6.11680.2191440.20021312X-RAY DIFFRACTION99
6.1168-29.04650.21541570.1981402X-RAY DIFFRACTION99

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