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- PDB-4o4k: DNA Double-Strand Break Repair Pathway Choice Is Directed by Dist... -

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Basic information

Entry
Database: PDB / ID: 4o4k
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 / DNA repair DNA double-strand break repair / 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 / Hydrolases; Acting on ester bonds / DNA replication / 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-2PK / : / DNA double-strand break repair protein Mre11
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 18, 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_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_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)77,8118
Polymers77,1502
Non-polymers6606
Water2,360131
1
A: Exonuclease, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9054
Polymers38,5751
Non-polymers3303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exonuclease, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9054
Polymers38,5751
Non-polymers3303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-46 kcal/mol
Surface area29700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.769, 113.154, 80.891
Angle α, β, γ (deg.)90.00, 101.47, 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-2PK / (5~{E})-2-azanylidene-5-[(4-hydroxyphenyl)methylidene]-1,3-thiazolidin-4-one


Mass: 220.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8N2O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.78 Å3/Da / Density % sol: 55.71 %
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: 2.1→50 Å / Num. all: 46357 / Num. obs: 46357 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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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: 2.1→37.409 Å / SU ML: 0.29 / σ(F): 0 / Phase error: 30.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2402 1870 4.29 %
Rwork0.1934 --
obs0.1955 43542 88.65 %
all-46357 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→37.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5150 0 34 131 5315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085304
X-RAY DIFFRACTIONf_angle_d1.2377188
X-RAY DIFFRACTIONf_dihedral_angle_d13.5291962
X-RAY DIFFRACTIONf_chiral_restr0.082800
X-RAY DIFFRACTIONf_plane_restr0.005925
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1002-2.1570.3121820.26771834X-RAY DIFFRACTION51
2.157-2.22050.29871000.252317X-RAY DIFFRACTION64
2.2205-2.29210.31551200.25042753X-RAY DIFFRACTION77
2.2921-2.3740.31531410.22693214X-RAY DIFFRACTION89
2.374-2.46910.27151530.22153292X-RAY DIFFRACTION92
2.4691-2.58140.30961560.23273385X-RAY DIFFRACTION95
2.5814-2.71750.30471520.23073426X-RAY DIFFRACTION95
2.7175-2.88770.28531610.22363537X-RAY DIFFRACTION97
2.8877-3.11050.27241590.22823542X-RAY DIFFRACTION98
3.1105-3.42340.2541600.21413601X-RAY DIFFRACTION99
3.4234-3.91830.24311620.18423566X-RAY DIFFRACTION99
3.9183-4.93480.20071630.15483623X-RAY DIFFRACTION100
4.9348-37.41490.19021610.16853582X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 16.9642 Å / Origin y: 456.2856 Å / Origin z: 19.7197 Å
111213212223313233
T0.2301 Å20.0488 Å20.0054 Å2-0.257 Å20.0528 Å2--0.2838 Å2
L0.1253 °2-0.0243 °20.1968 °2-0.1936 °2-0.093 °2--0.8086 °2
S-0.0111 Å °0.016 Å °0.0843 Å °-0.0454 Å °-0.0542 Å °-0.0059 Å °0.1265 Å °0.0976 Å °-0.0083 Å °
Refinement TLS groupSelection details: all

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