[English] 日本語
Yorodumi
- PDB-6x1y: Mre11 dimer in complex with small molecule modulator PFMI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6x1y
TitleMre11 dimer in complex with small molecule modulator PFMI
ComponentsNuclease SbcCD subunit D
KeywordsHYDROLASE / DNA REPAIR MRE11 THERMOPHILIC NUCLEASE / DNA DOUBLE-STRAND BREAK REPAIR
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-UKV / DNA double-strand break repair protein Mre11
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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)5R01CA117638-15 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)5P01CA092584-19 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)78,0446
Polymers77,1502
Non-polymers8934
Water1,56787
1
A: Nuclease SbcCD subunit D
hetero molecules

B: Nuclease SbcCD subunit D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0446
Polymers77,1502
Non-polymers8934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_343-x-2,y-1/2,-z-21
Buried area2500 Å2
ΔGint-11 kcal/mol
Surface area29710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.199, 109.147, 75.996
Angle α, β, γ (deg.)90.000, 99.934, 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:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid -2 through 158 or resid 160 through 801 or resid 501))A-2 - 158
121(chain 'A' and (resid -2 through 158 or resid 160 through 801 or resid 501))A160 - 324
131(chain 'A' and (resid -2 through 158 or resid 160 through 801 or resid 501))A501
141(chain 'A' and (resid -2 through 158 or resid 160 through 801 or resid 501))A801
211(chain 'B' and (resid -2 through 158 or resid 160 through 801 or resid 501))B-2 - 158
221(chain 'B' and (resid -2 through 158 or resid 160 through 801 or resid 501))B160 - 324
231(chain 'B' and (resid -2 through 158 or resid 160 through 801 or resid 501))B501
241(chain 'B' and (resid -2 through 158 or resid 160 through 801 or resid 501))B801

-
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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-UKV / (5Z)-5-[(3-methoxyphenyl)methylidene]-2-sulfanylidene-1,3-thiazolidin-4-one


Mass: 251.325 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H9NO2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 0.01 M CaCl2, 1% PEG 2000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.11585 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11585 Å / Relative weight: 1
ReflectionResolution: 2.35→44.1 Å / Num. obs: 58497 / % possible obs: 98.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 44.72 Å2 / Rpim(I) all: 0.049 / Rrim(I) all: 0.095 / Net I/σ(I): 29.3
Reflection shellResolution: 2.35→2.39 Å / Num. unique obs: 1542 / CC1/2: 0.636

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NZV

4nzv


Resolution: 2.35→44.1 Å / SU ML: 0.2929 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.2966
RfactorNum. reflection% reflection
Rfree0.2382 2561 4.95 %
Rwork0.2083 --
obs0.2098 51691 83.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 69.5 Å2
Refinement stepCycle: LAST / Resolution: 2.35→44.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5240 0 56 87 5383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00265426
X-RAY DIFFRACTIONf_angle_d0.65657346
X-RAY DIFFRACTIONf_chiral_restr0.0428804
X-RAY DIFFRACTIONf_plane_restr0.0028944
X-RAY DIFFRACTIONf_dihedral_angle_d18.83562044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.40.32481060.3212199X-RAY DIFFRACTION67.67
2.4-2.450.31151250.31282485X-RAY DIFFRACTION75.89
2.45-2.50.32741440.31532544X-RAY DIFFRACTION77.42
2.5-2.560.34091290.29052611X-RAY DIFFRACTION80.05
2.56-2.620.32751290.30132632X-RAY DIFFRACTION78.13
2.62-2.690.34331260.33792354X-RAY DIFFRACTION73.48
2.69-2.770.30431370.27212574X-RAY DIFFRACTION77.55
2.77-2.860.36781390.26222790X-RAY DIFFRACTION86.32
2.86-2.960.31831540.23762979X-RAY DIFFRACTION89.41
2.96-3.080.27861590.2292947X-RAY DIFFRACTION90.71
3.08-3.220.27981590.22943024X-RAY DIFFRACTION92.34
3.22-3.390.22651590.22052941X-RAY DIFFRACTION89.26
3.39-3.60.27891430.22572700X-RAY DIFFRACTION82.03
3.6-3.880.23111450.222662X-RAY DIFFRACTION82.05
3.88-4.270.20471510.17462853X-RAY DIFFRACTION86.5
4.27-4.890.18531470.14342899X-RAY DIFFRACTION89.33
4.89-6.160.17951580.16242974X-RAY DIFFRACTION90.91
6.16-44.10.18461510.16832962X-RAY DIFFRACTION89.74
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)
10.6658344801440.0266845725571-0.5317482949880.170088287902-0.3614701181760.501579689364-0.07206258062480.222695891676-0.222710347321-0.0793687964590.1154638057090.449463840944-0.0299785295105-0.2048043573360.07475287177080.3936948908840.1459445671770.04921759387650.3637442727620.04167584898680.314172896072-30.3034343877450.977363978-112.910309899
20.781038868435-0.26468351938-0.1629403618460.874464645429-1.269903078951.68312663216-0.006802045907030.0314421557275-0.196507105046-0.03236093718020.09074582500080.121505948470.002509179142820.1088810927291.15518759848E-50.3454923284650.1051353696540.02312782074960.3360838096040.02235699472510.352159558936-32.1301225391451.678321385-106.493080963
31.05750522285-0.112631570277-0.1612424525270.8030462795340.3156200120111.953527416340.106005788099-0.264202402655-0.0245897151540.183965798392-0.185238511772-0.1210839363450.03816834845090.798148873517-0.0006064507592010.3233532282890.0888159106164-0.0001206994038990.6107096761330.08776603355350.334759810535-12.9299321553451.998040505-106.747657449
41.78849286631-0.0704355036320.2726934326370.7067984121920.2099780626660.8431215894680.0924511706850.2581510092530.276635116673-0.564701006612-0.2518009367730.01512135455990.06200146252640.3368103288290.000721747631240.4480163412170.0930786816303-0.03198474961110.4689470472850.06847672381910.324202992582-30.3879545031463.091641291-126.938308631
50.21010223349-0.849527088114-0.001609617945941.39859321447-1.180642411690.889869676492-0.021472742586-0.09976915560230.09350469949420.09829257139620.1282288636050.109437518452-0.139866325086-0.142505314839-0.0004410080412440.246103199641-0.056118620459-0.01104113223880.21211450716-0.02313048989080.289349914118-33.0914842037506.025736116-69.9631868218
61.39984790435-0.269611403183-0.4987665719651.114661374060.4850788042731.730416909020.0379930854718-0.1344182489440.1258112043760.0300171165592-0.140224745478-0.2823773723350.0254560560230.467407303389-0.001020334548990.244645207498-0.0440466695918-0.02210069932780.3667193875860.04103758631790.376079663204-14.5392941903506.873405176-68.1635455854
70.887307872542-0.903626710539-0.04207424228381.16748912308-0.727091213410.5643189999970.2113478398490.1951769626630.147665532558-0.463769251951-0.256938938221-0.1234582908720.2080912530010.297355055727-0.000395483719730.4155414587090.0032621261459-0.02094204303630.3058247467510.01338080907930.368165880436-32.0473559277517.709953085-88.4824430202
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 109 )
3X-RAY DIFFRACTION3chain 'A' and (resid 110 through 215 )
4X-RAY DIFFRACTION4chain 'A' and (resid 216 through 324 )
5X-RAY DIFFRACTION5chain 'B' and (resid -2 through 109 )
6X-RAY DIFFRACTION6chain 'B' and (resid 110 through 215 )
7X-RAY DIFFRACTION7chain 'B' and (resid 216 through 324 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more