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- PDB-4o5g: DNA Double-Strand Break Repair Pathway Choice Is Directed by Dist... -

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Basic information

Entry
Database: PDB / ID: 4o5g
TitleDNA Double-Strand Break Repair Pathway Choice Is Directed by Distinct MRE11 Nuclease Activities
ComponentsExonuclease, putative
KeywordsDNA BINDING PROTEIN/inhibitor / DNA repair DNA double-strand break repair thermophilic MRE11 nuclease / DNA repair DNA double-strand break repair / DNA BINDING PROTEIN / DNA BINDING PROTEIN-inhibitor complex
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 / : / : / Mre11 accessory DNA binding capping domain / Mre11 C-terminal domain, bacteria / Nuclease SbcCD subunit D / : / Mre11 nuclease, N-terminal metallophosphatase domain / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 ...DNA double-strand break repair nuclease / : / : / Mre11 accessory DNA binding capping domain / Mre11 C-terminal domain, bacteria / 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
Chem-2PV / : / DNA double-strand break repair protein Mre11
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å
AuthorsShibata, A. / Moiani, D. / Arvai, A.S. / Perry, J. / Harding, S.M. / Genois, M. / Maity, R. / Rossum-Fikkert, S. / Kertokalio, A. / Romoli, F. ...Shibata, A. / Moiani, D. / Arvai, A.S. / Perry, J. / Harding, S.M. / Genois, M. / Maity, R. / Rossum-Fikkert, S. / Kertokalio, A. / Romoli, F. / Ismail, A. / Ismalaj, E. / Petricci, E. / Neale, M.J. / Bristow, R.G. / Masson, J. / Wyman, C. / Jeggo, P.A. / Tainer, J.A.
CitationJournal: Mol.Cell / Year: 2014
Title: DNA Double-Strand Break Repair Pathway Choice Is Directed by Distinct MRE11 Nuclease Activities.
Authors: Shibata, A. / Moiani, D. / Arvai, A.S. / Perry, J. / Harding, S.M. / Genois, M.M. / Maity, R. / van Rossum-Fikkert, S. / Kertokalio, A. / Romoli, F. / Ismail, A. / Ismalaj, E. / Petricci, E. ...Authors: Shibata, A. / Moiani, D. / Arvai, A.S. / Perry, J. / Harding, S.M. / Genois, M.M. / Maity, R. / van Rossum-Fikkert, S. / Kertokalio, A. / Romoli, F. / Ismail, A. / Ismalaj, E. / Petricci, E. / Neale, M.J. / Bristow, R.G. / Masson, J.Y. / Wyman, C. / Jeggo, P.A. / Tainer, J.A.
History
DepositionDec 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 2.0Feb 19, 2020Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / struct_ref_seq_dif
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Revision 2.1Sep 20, 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_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_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_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
B: Exonuclease, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8098
Polymers77,1502
Non-polymers6586
Water2,468137
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-45 kcal/mol
Surface area29320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.724, 113.423, 80.482
Angle α, β, γ (deg.)90.00, 101.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Exonuclease, putative


Mass: 38575.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: 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.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-2PV / (5~{E})-5-[(4-aminophenyl)methylidene]-2-azanylidene-1,3-thiazolidin-4-one


Mass: 219.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H9N3OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.77 Å3/Da / Density % sol: 55.58 %
Crystal growTemperature: 288 K / Method: vapor diffusion / pH: 6 / Details: pH 6, VAPOR DIFFUSION, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 37120 / Num. obs: 37120 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.38 Å / % possible all: 98.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4NZV

4nzv


Resolution: 2.301→46.055 Å / SU ML: 0.35 / σ(F): 1.35 / Phase error: 27.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2312 1848 4.99 %
Rwork0.1911 --
obs0.1932 37055 99.44 %
all-37120 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.301→46.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5150 0 34 137 5321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045304
X-RAY DIFFRACTIONf_angle_d0.8457188
X-RAY DIFFRACTIONf_dihedral_angle_d11.3751962
X-RAY DIFFRACTIONf_chiral_restr0.051800
X-RAY DIFFRACTIONf_plane_restr0.003925
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3011-2.36330.38641290.31452629X-RAY DIFFRACTION96
2.3633-2.43290.28571360.27172677X-RAY DIFFRACTION99
2.4329-2.51140.34941550.25822722X-RAY DIFFRACTION100
2.5114-2.60110.2951420.23882674X-RAY DIFFRACTION100
2.6011-2.70530.27941360.23132695X-RAY DIFFRACTION100
2.7053-2.82840.32261470.22712739X-RAY DIFFRACTION100
2.8284-2.97750.27811320.2182739X-RAY DIFFRACTION100
2.9775-3.1640.25731200.23282750X-RAY DIFFRACTION100
3.164-3.40820.271410.21372728X-RAY DIFFRACTION100
3.4082-3.75110.24531430.18672689X-RAY DIFFRACTION100
3.7511-4.29350.21291560.16872722X-RAY DIFFRACTION100
4.2935-5.4080.18121440.14832736X-RAY DIFFRACTION100
5.408-46.06470.18931670.17112707X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 64.7307 Å / Origin y: 456.3783 Å / Origin z: 19.5535 Å
111213212223313233
T0.3101 Å20.0316 Å20.0021 Å2-0.3382 Å20.0397 Å2--0.3777 Å2
L0.2089 °2-0.0532 °20.1744 °2-0.3777 °2-0.1179 °2--0.7428 °2
S-0.0051 Å °0.0078 Å °0.0768 Å °-0.0339 Å °-0.0558 Å °0.0054 Å °0.1238 Å °0.0703 Å °-0 Å °
Refinement TLS groupSelection details: all

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