[English] 日本語
Yorodumi
- PDB-4nzv: DNA Double-Strand Break Repair Pathway Choice Is Directed by Dist... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nzv
TitleDNA Double-Strand Break Repair Pathway Choice Is Directed by Distinct MRE11 Nuclease Activities
ComponentsExonuclease, putative
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 / : / : / 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
: / DNA double-strand break repair protein Mre11
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 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 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Exonuclease, putative
B: Exonuclease, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3706
Polymers77,1502
Non-polymers2204
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-40 kcal/mol
Surface area29820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.116, 109.949, 76.917
Angle α, β, γ (deg.)90.00, 100.21, 90.00
Int Tables number4
Space group name H-MP1211

-
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.51 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6
Details: pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 288K

-
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: 1.9→50 Å / Num. all: 60257 / Num. obs: 60257 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.078

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.901→44.482 Å / SU ML: 0.21 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2655 1802 3.31 %RANDOM
Rwork0.2312 ---
obs0.2323 54461 89.9 %-
all-54461 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.901→44.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5220 0 4 305 5529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045347
X-RAY DIFFRACTIONf_angle_d0.897239
X-RAY DIFFRACTIONf_dihedral_angle_d12.8372001
X-RAY DIFFRACTIONf_chiral_restr0.066802
X-RAY DIFFRACTIONf_plane_restr0.004934
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9009-1.95230.32521200.31093376X-RAY DIFFRACTION75
1.9523-2.00980.32051250.26373640X-RAY DIFFRACTION81
2.0098-2.07460.31921250.24963759X-RAY DIFFRACTION84
2.0746-2.14880.251310.2363907X-RAY DIFFRACTION87
2.1488-2.23480.25011340.23713942X-RAY DIFFRACTION88
2.2348-2.33650.30751410.23744081X-RAY DIFFRACTION91
2.3365-2.45970.24461440.23724054X-RAY DIFFRACTION91
2.4597-2.61380.27231430.23694198X-RAY DIFFRACTION93
2.6138-2.81560.25711390.24174207X-RAY DIFFRACTION94
2.8156-3.09880.25621430.25164305X-RAY DIFFRACTION95
3.0988-3.54710.27281520.23584383X-RAY DIFFRACTION97
3.5471-4.46830.26081540.20134411X-RAY DIFFRACTION98
4.4683-44.4940.2491510.22424396X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 4.1953 Å / Origin y: 453.3339 Å / Origin z: 94.2115 Å
111213212223313233
T0.2091 Å20.0101 Å2-0.0144 Å2-0.2041 Å20.0058 Å2--0.2729 Å2
L0.6654 °20.0581 °2-0.1747 °2-0.4138 °2-0.1178 °2--1.949 °2
S-0.0377 Å °0.0739 Å °-0.03 Å °-0.0806 Å °-0.031 Å °-0.0209 Å °0.0451 Å °0.013 Å °0.0689 Å °
Refinement TLS groupSelection details: all

+
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://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