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- PDB-6x1z: Mre11 dimer in complex with small molecule modulator PFMJ -

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Basic information

Entry
Database: PDB / ID: 6x1z
TitleMre11 dimer in complex with small molecule modulator PFMJ
ComponentsNuclease SbcCD subunit D
KeywordsHYDROLASE/INHIBITOR / DNA REPAIR MRE11 THERMOPHILIC NUCLEASE / DNA DOUBLE-STRAND BREAK REPAIR / 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-UL1 / DNA double-strand break repair protein Mre11
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsArvai, A.S. / Moiani, D. / Tainer, J.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)5P01CA092584-19 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)5R01CA117638-15 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)5R35CA220430-02 United States
CitationJournal: Prog.Biophys.Mol.Biol. / Year: 2021
Title: Fragment- and structure-based drug discovery for developing therapeutic agents targeting the DNA Damage Response.
Authors: Wilson 3rd, D.M. / Deacon, A.M. / Duncton, M.A.J. / Pellicena, P. / Georgiadis, M.M. / Yeh, A.P. / Arvai, A.S. / Moiani, D. / Tainer, J.A. / Das, D.
History
DepositionMay 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 16, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)78,1528
Polymers77,1502
Non-polymers1,0026
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-29 kcal/mol
Surface area29710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.260, 109.440, 75.650
Angle α, β, γ (deg.)90.000, 99.970, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISPROPRO(chain 'A' and (resid -1 through 260 or resid 262 through 324 or resid 601 through 801))AA-1 - 26011 - 272
12TYRTYRGLUGLU(chain 'A' and (resid -1 through 260 or resid 262 through 324 or resid 601 through 801))AA262 - 324274 - 336
13UL1UL1UL1UL1(chain 'A' and (resid -1 through 260 or resid 262 through 324 or resid 601 through 801))AC601
14HOHHOHHOHHOH(chain 'A' and (resid -1 through 260 or resid 262 through 324 or resid 601 through 801))AI801
21HISHISPROPRO(chain 'B' and (resid -1 through 193 or (resid 194...BB-1 - 26011 - 272
22TYRTYRGLUGLU(chain 'B' and (resid -1 through 193 or (resid 194...BB262 - 324274 - 336
23UL1UL1UL1UL1(chain 'B' and (resid -1 through 193 or (resid 194...BF601
24HOHHOHHOHHOH(chain 'B' and (resid -1 through 193 or (resid 194...BJ801

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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) / Gene: sbcD, TM_1635 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1X0
#2: Chemical ChemComp-UL1 / (5Z)-5-[(3,4-dimethoxyphenyl)methylidene]-2-sulfanylidene-1,3-thiazolidin-4-one


Mass: 281.351 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H11NO3S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.5 Å3/Da / Density % sol: 50.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 0.02 M MgCl2, 0.5% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.115842 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115842 Å / Relative weight: 1
ReflectionResolution: 1.9→37.25 Å / Num. obs: 56599 / % possible obs: 95.2 % / Redundancy: 5.97 % / Biso Wilson estimate: 28.89 Å2 / CC1/2: 0.991 / Rrim(I) all: 0.107 / Net I/σ(I): 9.39
Reflection shellResolution: 1.9→1.95 Å / Num. unique obs: 2886 / CC1/2: 0.695

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NZV

4nzv


Resolution: 1.9→37.25 Å / SU ML: 0.2448 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.0386
RfactorNum. reflection% reflection
Rfree0.2386 1791 3.51 %
Rwork0.1999 --
obs0.2012 51050 85.9 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.88 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5281 0 62 343 5686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00845473
X-RAY DIFFRACTIONf_angle_d1.06537402
X-RAY DIFFRACTIONf_chiral_restr0.0622806
X-RAY DIFFRACTIONf_plane_restr0.0063949
X-RAY DIFFRACTIONf_dihedral_angle_d20.41572076
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.426730.42832073X-RAY DIFFRACTION47.18
1.95-2.010.36561090.31723035X-RAY DIFFRACTION69.43
2.01-2.080.28631330.3053439X-RAY DIFFRACTION77.97
2.08-2.150.28931320.24893638X-RAY DIFFRACTION82.75
2.15-2.240.24441300.23763634X-RAY DIFFRACTION82.94
2.24-2.340.3281340.25343655X-RAY DIFFRACTION82.73
2.34-2.460.22611410.21044011X-RAY DIFFRACTION91.33
2.46-2.610.24361500.20434116X-RAY DIFFRACTION93.43
2.61-2.820.21691520.20244173X-RAY DIFFRACTION94.66
2.82-3.10.22281550.20284275X-RAY DIFFRACTION96.96
3.1-3.550.22161600.18894360X-RAY DIFFRACTION98.41
3.55-4.470.20021580.15914381X-RAY DIFFRACTION99.04
4.47-37.250.241640.17564469X-RAY DIFFRACTION99.27
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.0156728658494-0.102006474097-0.1512602423040.181004146530.3832783428390.411425715062-0.0235566963971-0.0231365009809-0.06413483258080.135887238909-0.00468282329139-0.004869976788920.03284882301590.04905012769572.82488422876E-50.193473928517-0.0190334594288-0.01412609411170.1338430966340.0001363616279430.2236341067381.76175758012447.27200187110.608400564
21.256450719460.475933890785-0.423861683020.9883862027480.6255138550411.41221383762-0.03493362159070.07827998126230.0510812202473-0.106613451910.0917995093834-0.0171510301074-0.07215623722130.0232324767837-1.15191761591E-50.148264426268-0.0132578749968-0.0155161754780.1180085437930.01582725247460.1728054322162.12623612459448.959956086103.860462228
31.87135766411-0.006110988588060.1446478770630.705090306861-0.190993604140.9792991387430.0640031458775-0.01979174837560.1443736337830.125308309344-0.1868917090410.191474162137-0.0341752506931-0.369639384398-0.1266024379840.140865150222-0.02032961400430.007847491060440.187696437634-0.0496723460160.290621276813-16.7915288026450.736733285106.024453092
40.7390978632911.023792354390.03562181839241.228571693050.2031562656240.6672726396460.212908002375-0.2862133727790.05263534032120.421146857918-0.2731612910330.168899882302-0.0376390491581-0.206527288680.01732073329340.247209947503-0.042732854239-0.005659953248280.174695136487-0.02855264857150.1618741648271.8933049241460.87293972125.323076267
50.139778974573-0.313446781243-0.305173590838-0.0231518347306-0.04887229221111.19690132236-0.04390333533230.194776150665-0.0742245303830.2694670598970.02944383819430.226023795799-0.205829223242-0.1279209548910.003307797488960.227748655632-0.03723331599390.0004589645427210.314158046955-0.02537060847790.2872204551597.79064702772449.39584217473.2735953877
61.32881593061-0.30540907149-0.4832471129770.865342785792-0.7172512230231.7012336276-0.07529803633460.0879670806791-0.04580758208650.07716413756690.08501032697340.127923148614-0.03504790015410.08087501443721.22011633455E-50.222914225829-0.03457079249290.01249925469040.228327375868-0.02444388697520.2428928474657.26527887268448.85554377181.2681503682
71.89577746543-0.66329191003-0.04653330809140.504145264172-0.07770975243131.71567539254-0.0361367167223-0.1132108498130.134145182003-0.0420908663143-0.0976077098394-0.213376490338-0.03183870998270.566205896742-0.0004531049271550.240900682171-0.01081572700470.00955585145330.4068258435790.04480934748540.28784492165926.4911007196450.69488807879.3076238607
80.8973960653280.0981010480606-0.02643335967080.0254315839909-0.4207517804420.899978447569-0.04947460711460.2983121283730.0414093828321-0.32120790931-0.0578276286442-0.09208852462780.09964998596010.290916540378-0.01254020785280.3267032776060.007390095754520.04037274210410.4597136656-0.04720298926530.21324805799916.5851647187447.82520378566.3030397712
90.624347969966-0.05587142418980.3389239116170.3884795117680.3882253855980.2347833389140.008928841308330.2034466920910.297300235689-0.338779909423-0.1984292473890.0136755187848-0.144103920049-0.018056536646-0.0007950901472230.517018331776-0.00218909610761-0.1242687687830.3581556628860.08055481189370.374654625015-0.303734737151472.38077344454.5583752681
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 121 )
3X-RAY DIFFRACTION3chain 'A' and (resid 122 through 215 )
4X-RAY DIFFRACTION4chain 'A' and (resid 216 through 324 )
5X-RAY DIFFRACTION5chain 'B' and (resid -1 through 30 )
6X-RAY DIFFRACTION6chain 'B' and (resid 31 through 121 )
7X-RAY DIFFRACTION7chain 'B' and (resid 122 through 210 )
8X-RAY DIFFRACTION8chain 'B' and (resid 211 through 266 )
9X-RAY DIFFRACTION9chain 'B' and (resid 267 through 324 )

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