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- PDB-6asc: Mre11 dimer in complex with Endonuclease inhibitor PFM04 -

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Basic information

Entry
Database: PDB / ID: 6asc
TitleMre11 dimer in complex with Endonuclease inhibitor PFM04
ComponentsNuclease SbcCD subunit D
Keywordshydrolase/hydrolase inhibitor / DNA REPAIR MRE11 THERMOPHILIC NUCLEASE DNA DOUBLE-STRAND BREAK REPAIR HYDROLASE / hydrolase-hydrolase 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 / 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-BU7 / : / DNA double-strand break repair protein Mre11
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.15 Å
AuthorsMoiani, D. / Arvai, A.S. / Tainer, J.A.
CitationJournal: Meth. Enzymol. / Year: 2018
Title: Targeting Allostery with Avatars to Design Inhibitors Assessed by Cell Activity: Dissecting MRE11 Endo- and Exonuclease Activities.
Authors: Moiani, D. / Ronato, D.A. / Brosey, C.A. / Arvai, A.S. / Syed, A. / Masson, J.Y. / Petricci, E. / Tainer, J.A.
History
DepositionAug 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
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.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclease SbcCD subunit D
B: Nuclease SbcCD subunit D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0199
Polymers77,1502
Non-polymers8697
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-47 kcal/mol
Surface area29720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.053, 112.682, 81.162
Angle α, β, γ (deg.)90.00, 100.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nuclease SbcCD subunit D


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: sbcD, 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: isolated from a natural source / Formula: Mn
#3: Chemical ChemComp-BU7 / (5E)-3-butyl-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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.87 Å3/Da / Density % sol: 57.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: We added 5mM PFM04 (dissolved in DMSO) to 10 mg/ml TmMre11. The mother liquor was 10% PEG3350, 20 mM CaCl2, 0.1 M Mes pH 6.5. This was mixed 1:1 with the protein:inhibitor complex and set up ...Details: We added 5mM PFM04 (dissolved in DMSO) to 10 mg/ml TmMre11. The mother liquor was 10% PEG3350, 20 mM CaCl2, 0.1 M Mes pH 6.5. This was mixed 1:1 with the protein:inhibitor complex and set up as hanging drop vapor diffusion. For cryoprotection, 20% ethylene glycol was added to the mother liquor.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.11583 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 43590 / % possible obs: 94.2 % / Redundancy: 4.8 % / Net I/σ(I): 46.71

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2580: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 2.15→46.038 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2318 3303 4.56 %
Rwork0.1969 --
obs0.1984 72439 79.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→46.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5184 0 46 142 5372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045351
X-RAY DIFFRACTIONf_angle_d0.7897247
X-RAY DIFFRACTIONf_dihedral_angle_d15.5513216
X-RAY DIFFRACTIONf_chiral_restr0.046800
X-RAY DIFFRACTIONf_plane_restr0.004932
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.18080.317750.30711480X-RAY DIFFRACTION40
2.1808-2.21330.3576760.31051645X-RAY DIFFRACTION45
2.2133-2.24790.35930.30021832X-RAY DIFFRACTION51
2.2479-2.28480.32661010.27082095X-RAY DIFFRACTION57
2.2848-2.32410.3771260.27362397X-RAY DIFFRACTION67
2.3241-2.36640.32171230.27342642X-RAY DIFFRACTION73
2.3664-2.41190.32631280.2442756X-RAY DIFFRACTION75
2.4119-2.46110.30191180.24912743X-RAY DIFFRACTION76
2.4611-2.51470.28581480.23722884X-RAY DIFFRACTION80
2.5147-2.57320.2651410.23542874X-RAY DIFFRACTION80
2.5732-2.63750.29311420.23972986X-RAY DIFFRACTION82
2.6375-2.70880.24751460.23133080X-RAY DIFFRACTION84
2.7088-2.78850.29451500.24413106X-RAY DIFFRACTION86
2.7885-2.87850.26181440.23073066X-RAY DIFFRACTION86
2.8785-2.98140.27141570.22813232X-RAY DIFFRACTION88
2.9814-3.10070.25061510.23693187X-RAY DIFFRACTION89
3.1007-3.24180.27961610.22443244X-RAY DIFFRACTION90
3.2418-3.41260.24831620.22873339X-RAY DIFFRACTION92
3.4126-3.62640.25191530.20263338X-RAY DIFFRACTION92
3.6264-3.90620.25451550.18663373X-RAY DIFFRACTION93
3.9062-4.29910.15811660.16263402X-RAY DIFFRACTION94
4.2991-4.92050.18981550.14533446X-RAY DIFFRACTION95
4.9205-6.1970.18961600.17643473X-RAY DIFFRACTION96
6.197-46.04820.20651720.16873516X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 17.4429 Å / Origin y: 456.001 Å / Origin z: 19.7368 Å
111213212223313233
T0.3106 Å20.0215 Å2-0.0042 Å2-0.3418 Å20.0502 Å2--0.3719 Å2
L0.2663 °20.1023 °20.0735 °2-0.363 °2-0.1455 °2--0.3622 °2
S-0.0286 Å °0.0153 Å °0.0706 Å °-0.032 Å °-0.0675 Å °-0.0318 Å °0.1227 Å °-0.0405 Å °-0.0125 Å °
Refinement TLS groupSelection details: not resname HOH

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