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- PDB-4o43: DNA Double-Strand Break Repair Pathway Choice Is Directed by Dist... -

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Basic information

Entry
Database: PDB / ID: 4o43
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-inhibitor complex
Function / homology
Function and homology information


DNA exonuclease activity / 3'-5' exonuclease activity / endonuclease activity / DNA recombination / DNA replication / DNA repair / DNA binding / metal ion binding
Similarity search - Function
DNA double-strand break repair nuclease / 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 ...DNA double-strand break repair nuclease / 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-2PW / : / Nuclease SbcCD subunit D
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)77,9578
Polymers77,1502
Non-polymers8076
Water2,198122
1
A: Exonuclease, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2725
Polymers38,5751
Non-polymers6974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exonuclease, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6853
Polymers38,5751
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.060, 113.943, 81.566
Angle α, β, γ (deg.)90.00, 100.31, 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-2PW / (5~{E})-3-[(2~{R})-butan-2-yl]-5-[(4-hydroxyphenyl)methylidene]-2-sulfanylidene-1,3-thiazolidin-4-one


Mass: 293.404 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15NO2S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.85 Å3/Da / Density % sol: 56.81 %
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: 2.4→50 Å / Num. all: 32631 / Num. obs: 32631 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.49 Å / % possible all: 99.5

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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: 4NZV

4nzv


Resolution: 2.4→37.88 Å / SU ML: 0.33 / σ(F): 0 / Phase error: 28.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2556 1241 5.01 %RANDOM
Rwork0.1945 ---
obs0.1976 24749 73.25 %-
all-32631 --
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→37.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5154 0 42 122 5318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045316
X-RAY DIFFRACTIONf_angle_d0.8097205
X-RAY DIFFRACTIONf_dihedral_angle_d10.8221969
X-RAY DIFFRACTIONf_chiral_restr0.05802
X-RAY DIFFRACTIONf_plane_restr0.002926
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.49620.3499510.2163940X-RAY DIFFRACTION27
2.4962-2.60970.3205750.2261410X-RAY DIFFRACTION40
2.6097-2.74730.33291130.24322198X-RAY DIFFRACTION62
2.7473-2.91940.29451640.24563065X-RAY DIFFRACTION86
2.9194-3.14470.30281740.23883318X-RAY DIFFRACTION94
3.1447-3.46090.31081780.22693399X-RAY DIFFRACTION95
3.4609-3.96130.24461100.19522077X-RAY DIFFRACTION58
3.9613-4.9890.1931870.15123508X-RAY DIFFRACTION98
4.989-37.88470.22351890.16343593X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 17.4074 Å / Origin y: 456.3056 Å / Origin z: 20.0226 Å
111213212223313233
T0.0859 Å20.0117 Å20.0015 Å2-0.089 Å20.033 Å2--0.125 Å2
L0.186 °20.0796 °20.1434 °2-0.2104 °2-0.1325 °2--0.3306 °2
S0.0022 Å °-0.0187 Å °0.0472 Å °-0.0236 Å °-0.0567 Å °-0.054 Å °0.1129 Å °-0.0298 Å °-0.219 Å °
Refinement TLS groupSelection details: all

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