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- PDB-4fcx: S.pombe Mre11 apoenzym -

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Basic information

Entry
Database: PDB / ID: 4fcx
TitleS.pombe Mre11 apoenzym
ComponentsDNA repair protein rad32
KeywordsHYDROLASE / DNA double-strand break repair / Nuclease
Function / homology
Function and homology information


Cytosolic sensors of pathogen-associated DNA / DNA Damage/Telomere Stress Induced Senescence / HDR through MMEJ (alt-NHEJ) / Sensing of DNA Double Strand Breaks / Processing of DNA double-strand break ends / mitochondrial double-strand break repair via homologous recombination / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Mre11 complex / meiotic DNA double-strand break formation / chromosome, telomeric repeat region ...Cytosolic sensors of pathogen-associated DNA / DNA Damage/Telomere Stress Induced Senescence / HDR through MMEJ (alt-NHEJ) / Sensing of DNA Double Strand Breaks / Processing of DNA double-strand break ends / mitochondrial double-strand break repair via homologous recombination / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Mre11 complex / meiotic DNA double-strand break formation / chromosome, telomeric repeat region / DNA end binding / DNA double-strand break processing / Y-form DNA binding / single-stranded DNA endodeoxyribonuclease activity / double-strand break repair involved in meiotic recombination / double-stranded DNA 3'-5' DNA exonuclease activity / nuclease activity / single-stranded DNA 3'-5' DNA exonuclease activity / reciprocal meiotic recombination / mitotic intra-S DNA damage checkpoint signaling / mitotic G2 DNA damage checkpoint signaling / telomere maintenance / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / double-strand break repair / site of double-strand break / 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
: / DNA repair protein rad32
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSchiller, C.B. / Lammens, K. / Hopfner, K.P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structure of Mre11-Nbs1 complex yields insights into ataxia-telangiectasia-like disease mutations and DNA damage signaling.
Authors: Schiller, C.B. / Lammens, K. / Guerini, I. / Coordes, B. / Feldmann, H. / Schlauderer, F. / Mockel, C. / Schele, A. / Strasser, K. / Jackson, S.P. / Hopfner, K.P.
History
DepositionMay 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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

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Assembly

Deposited unit
B: DNA repair protein rad32
A: DNA repair protein rad32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,5436
Polymers91,3232
Non-polymers2204
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-54 kcal/mol
Surface area33570 Å2
MethodPISA
2
A: DNA repair protein rad32
hetero molecules

B: DNA repair protein rad32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,5436
Polymers91,3232
Non-polymers2204
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
Buried area3110 Å2
ΔGint-30 kcal/mol
Surface area35040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.408, 82.262, 164.296
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 DNA repair protein rad32 /


Mass: 45661.492 Da / Num. of mol.: 2 / Fragment: Mre11 amino acids 15-413
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: rad32, SPAC13C5.07 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09683
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn

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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: 2.83 Å3/Da / Density % sol: 56.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20mM HEPES 300mM NaCl, 0.1mM EDTA, 1mM MnCl2, 2mM beta-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2008
RadiationMonochromator: Si monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→46 Å / Num. all: 21467 / Num. obs: 21028 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3→3.18 Å / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.7.3_928refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→21.842 Å / SU ML: 0.49 / σ(F): 1.99 / Phase error: 29.84 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2858 1978 9.45 %
Rwork0.2269 --
obs0.2324 20939 98.12 %
all-21467 -
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.986 Å2 / ksol: 0.295 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.1152 Å20 Å2-0 Å2
2--17.7494 Å2-0 Å2
3----22.6449 Å2
Refinement stepCycle: LAST / Resolution: 3→21.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5896 0 4 0 5900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086029
X-RAY DIFFRACTIONf_angle_d1.218177
X-RAY DIFFRACTIONf_dihedral_angle_d16.6962239
X-RAY DIFFRACTIONf_chiral_restr0.081912
X-RAY DIFFRACTIONf_plane_restr0.0051061
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0005-3.07530.45651160.34661322X-RAY DIFFRACTION95
3.0753-3.15820.39291640.3091320X-RAY DIFFRACTION99
3.1582-3.25090.34391220.28771345X-RAY DIFFRACTION99
3.2509-3.35540.31731460.27691355X-RAY DIFFRACTION99
3.3554-3.47490.35721430.25641360X-RAY DIFFRACTION99
3.4749-3.61340.33651440.24151339X-RAY DIFFRACTION99
3.6134-3.77710.28971380.22661335X-RAY DIFFRACTION99
3.7771-3.97510.2331300.22041372X-RAY DIFFRACTION99
3.9751-4.22250.28261480.2021357X-RAY DIFFRACTION98
4.2225-4.54580.26111470.1871326X-RAY DIFFRACTION98
4.5458-4.99830.25551380.19071362X-RAY DIFFRACTION98
4.9983-5.71020.27281490.20441372X-RAY DIFFRACTION98
5.7102-7.15210.31831460.24671383X-RAY DIFFRACTION98
7.1521-21.84290.23551470.21771413X-RAY DIFFRACTION94

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