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- PDB-4fbk: Crystal structure of a covalently fused Nbs1-Mre11 complex with o... -

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Basic information

Entry
Database: PDB / ID: 4fbk
TitleCrystal structure of a covalently fused Nbs1-Mre11 complex with one manganese ion per active site
ComponentsDNA repair and telomere maintenance protein nbs1,DNA repair protein rad32 CHIMERIC PROTEIN
KeywordsHYDROLASE / PROTEIN BINDING / DNA double-strand break repair / Nuclease / Schizosaccharomyces pombe
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 / chromosome, telomeric repeat region / meiotic DNA double-strand break formation ...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 / chromosome, telomeric repeat region / meiotic DNA double-strand break formation / phosphorylation-dependent protein binding / DNA end binding / Y-form DNA binding / chromatin-protein adaptor activity / double-strand break repair involved in meiotic recombination / DNA double-strand break processing / nuclease activity / single-stranded DNA endodeoxyribonuclease activity / double-stranded DNA 3'-5' DNA exonuclease activity / telomere maintenance via recombination / single-stranded DNA 3'-5' DNA exonuclease activity / reciprocal meiotic recombination / mitotic intra-S DNA damage checkpoint signaling / DNA duplex unwinding / protein localization to chromosome, telomeric region / 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 / damaged DNA binding / molecular adaptor activity / DNA repair / nucleus
Similarity search - Function
Mre11, capping domain / Nibrin-related / 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 ...Mre11, capping domain / Nibrin-related / 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 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / SMAD/FHA domain superfamily / Metallo-dependent phosphatase-like / BRCT domain superfamily / 4-Layer Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / DNA repair and telomere maintenance protein nbs1 / DNA repair protein rad32
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.379 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 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Jul 26, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Feb 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_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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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
A: DNA repair and telomere maintenance protein nbs1,DNA repair protein rad32 CHIMERIC PROTEIN
B: DNA repair and telomere maintenance protein nbs1,DNA repair protein rad32 CHIMERIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,1988
Polymers106,7042
Non-polymers4946
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-98 kcal/mol
Surface area36660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.261, 78.872, 222.678
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 and telomere maintenance protein nbs1,DNA repair protein rad32 CHIMERIC PROTEIN


Mass: 53351.914 Da / Num. of mol.: 2
Fragment: UNP O43070 residues 474-531, UNP Q09683 residues 15-413
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: O43070, UniProt: Q09683
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 MM Tri Na Citrate pH 5.0, 200 mM ammonium sulfate, 13% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 14, 2009
RadiationMonochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.379→47.884 Å / Num. all: 43368 / Num. obs: 43368 / % possible obs: 99.47 % / Observed criterion σ(I): 3

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XDSdata scaling
RefinementResolution: 2.379→47.884 Å / SU ML: 0.36 / σ(F): 1.34 / Phase error: 24.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2417 2000 4.61 %
Rwork0.2223 --
obs0.2232 43364 99.48 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.616 Å2 / ksol: 0.315 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.5387 Å20 Å2-0 Å2
2--6.9082 Å2-0 Å2
3----4.3696 Å2
Refinement stepCycle: LAST / Resolution: 2.379→47.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6702 0 22 210 6934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126867
X-RAY DIFFRACTIONf_angle_d1.7779313
X-RAY DIFFRACTIONf_dihedral_angle_d15.7432571
X-RAY DIFFRACTIONf_chiral_restr0.1231029
X-RAY DIFFRACTIONf_plane_restr0.011214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3791-2.43860.34411310.31542725X-RAY DIFFRACTION93
2.4386-2.50450.31421410.28592909X-RAY DIFFRACTION100
2.5045-2.57820.2811410.2772908X-RAY DIFFRACTION100
2.5782-2.66140.28831430.26372943X-RAY DIFFRACTION100
2.6614-2.75650.31551420.2552955X-RAY DIFFRACTION100
2.7565-2.86690.30491410.25362913X-RAY DIFFRACTION100
2.8669-2.99730.32081410.25212934X-RAY DIFFRACTION100
2.9973-3.15530.24981440.24362950X-RAY DIFFRACTION100
3.1553-3.3530.27351420.23082959X-RAY DIFFRACTION100
3.353-3.61180.22921440.22872953X-RAY DIFFRACTION100
3.6118-3.97510.23711440.2062998X-RAY DIFFRACTION100
3.9751-4.54990.20061440.17562989X-RAY DIFFRACTION100
4.5499-5.73090.17631480.18323032X-RAY DIFFRACTION100
5.7309-47.8940.22951540.2243196X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 55.8517 Å / Origin y: 2.2775 Å / Origin z: 30.6224 Å
111213212223313233
T0.1843 Å20.0256 Å2-0.0117 Å2-0.227 Å20.0838 Å2--0.2419 Å2
L0.3502 °20.1511 °20.3903 °2-0.4584 °2-0.0975 °2--0.7208 °2
S0.0703 Å °0.0057 Å °-0.0627 Å °-0.0318 Å °-0.0388 Å °-0.001 Å °0.0175 Å °0.1166 Å °0.0673 Å °
Refinement TLS groupSelection details: all

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