[English] 日本語
Yorodumi
- PDB-7dog: Crystal structure of a nuclease and capping domain of SbcD from S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dog
TitleCrystal structure of a nuclease and capping domain of SbcD from Staphylococcus aureus
ComponentsNuclease SbcCD subunit D
KeywordsHYDROLASE / DNA nuclease / endonuclease / exonuclease / DNA repair
Function / homology
Function and homology information


3'-5' exonuclease activity / endonuclease activity / DNA recombination / DNA replication
Similarity search - Function
: / Nuclease SbcCD subunit D, C-terminal domain / Type 5 capsule protein repressor C-terminal domain / Nuclease SbcCD subunit D / : / Mre11 nuclease, N-terminal metallophosphatase domain / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
: / Nuclease SbcCD subunit D
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsLee, J. / Ha, N.-C.
CitationJournal: J.Microbiol / Year: 2021
Title: Crystal structure of the nuclease and capping domain of SbcD from Staphylococcus aureus.
Authors: Lee, J. / Jo, I. / Ahn, J. / Hong, S. / Jeong, S. / Kwon, A. / Ha, N.C.
History
DepositionDec 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_scat_Cromer_Mann_a5 / _atom_type.pdbx_scat_Cromer_Mann_b5 ..._atom_type.pdbx_scat_Cromer_Mann_a5 / _atom_type.pdbx_scat_Cromer_Mann_b5 / _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)73,8596
Polymers73,6402
Non-polymers2204
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-45 kcal/mol
Surface area27250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.906, 89.465, 116.575
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Nuclease SbcCD subunit D


Mass: 36819.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Strain: Mu50 / Gene: sbcD, SAV1345 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99UD1
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop
Details: 2% (v/v) TacsimateTM (pH 6.0), 0.1 M Bis-Tris (pH 7.0), 18% (w/v) polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 16408 / % possible obs: 93.8 % / Redundancy: 5.5 % / Biso Wilson estimate: 46.69 Å2 / CC1/2: 0.989 / CC star: 0.997 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.051 / Rrim(I) all: 0.143 / Net I/σ(I): 10.7
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 749 / CC1/2: 0.752 / CC star: 0.926 / Rpim(I) all: 0.138 / Rrim(I) all: 0.297 / % possible all: 86.7

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6s6v

6s6v


Resolution: 2.91→48.84 Å / SU ML: 0.2667 / Cross valid method: FREE R-VALUE / σ(F): 1.59 / Phase error: 21.0164
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2491 774 5.04 %
Rwork0.1918 14576 -
obs0.1946 15350 87.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.64 Å2
Refinement stepCycle: LAST / Resolution: 2.91→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5129 0 4 0 5133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00295237
X-RAY DIFFRACTIONf_angle_d0.57627092
X-RAY DIFFRACTIONf_chiral_restr0.0467800
X-RAY DIFFRACTIONf_plane_restr0.0033911
X-RAY DIFFRACTIONf_dihedral_angle_d11.1912680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91-3.090.2845870.23611726X-RAY DIFFRACTION62.63
3.09-3.330.29261210.22652161X-RAY DIFFRACTION79.65
3.33-3.660.27091290.20322484X-RAY DIFFRACTION90.63
3.67-4.190.23331300.18052655X-RAY DIFFRACTION95.84
4.2-5.280.2471390.16582720X-RAY DIFFRACTION97.05
5.28-48.840.22611680.19252830X-RAY DIFFRACTION97.62

+
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