[English] 日本語
Yorodumi
- PDB-8ioo: Crystal structure of Deinococcus radiodurans RecJ-like protein in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ioo
TitleCrystal structure of Deinococcus radiodurans RecJ-like protein in complex with Mg2+
ComponentsRecJ-like protein
KeywordsHYDROLASE / RNase / nuclease
Function / homologyDDH domain / DHH family / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / nucleic acid binding / Uncharacterized protein
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCheng, K.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100017 China
National Natural Science Foundation of China (NSFC)32270043 China
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Structural and functional investigation of the DHH/DHHA1 family proteins in Deinococcus radiodurans.
Authors: Wang, Y. / Hao, W. / Guo, Z. / Sun, Y. / Wu, Y. / Sun, Y. / Gao, T. / Luo, Y. / Jin, L. / Yang, J. / Cheng, K.
History
DepositionMar 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RecJ-like protein
B: RecJ-like protein
C: RecJ-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,88014
Polymers107,2543
Non-polymers62611
Water7,927440
1
A: RecJ-like protein
B: RecJ-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,98410
Polymers71,5022
Non-polymers4818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-103 kcal/mol
Surface area27320 Å2
MethodPISA
2
C: RecJ-like protein
hetero molecules

C: RecJ-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7928
Polymers71,5022
Non-polymers2896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4820 Å2
ΔGint-117 kcal/mol
Surface area27160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.897, 124.842, 80.917
Angle α, β, γ (deg.)90.000, 92.720, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein RecJ-like protein


Mass: 35751.203 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: DR_0826 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RW43
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 3.72 Å3/Da / Density % sol: 66.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 1.4 M MgSO4, 0.08 M MES (pH 6.5), 15% (v/v) glycerol

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→42.04 Å / Num. obs: 106336 / % possible obs: 99.5 % / Redundancy: 2.9 % / Biso Wilson estimate: 36.92 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 8.7
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.358 / Num. unique obs: 7618

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→42.04 Å / SU ML: 0.2444 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3723
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2438 5046 4.96 %
Rwork0.2276 96759 -
obs0.2284 101805 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.73 Å2
Refinement stepCycle: LAST / Resolution: 2→42.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7295 0 31 440 7766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00957458
X-RAY DIFFRACTIONf_angle_d1.244610174
X-RAY DIFFRACTIONf_chiral_restr0.07911157
X-RAY DIFFRACTIONf_plane_restr0.01581361
X-RAY DIFFRACTIONf_dihedral_angle_d16.02162678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.36921820.34783223X-RAY DIFFRACTION98.72
2.02-2.050.31511570.33073176X-RAY DIFFRACTION98.9
2.05-2.070.34021350.31533238X-RAY DIFFRACTION98.71
2.07-2.10.31761700.31373167X-RAY DIFFRACTION98.96
2.1-2.130.3661550.30323243X-RAY DIFFRACTION99.36
2.13-2.150.28971670.28413174X-RAY DIFFRACTION99.52
2.15-2.190.29511690.27843232X-RAY DIFFRACTION99.62
2.19-2.220.2841640.26923180X-RAY DIFFRACTION99.58
2.22-2.250.28591870.26553227X-RAY DIFFRACTION99.33
2.25-2.290.28551600.25713204X-RAY DIFFRACTION99.44
2.29-2.330.25891550.25653208X-RAY DIFFRACTION99.44
2.33-2.370.26961870.25723191X-RAY DIFFRACTION99.62
2.37-2.420.26091580.26643233X-RAY DIFFRACTION99.68
2.42-2.470.29531890.27423230X-RAY DIFFRACTION99.77
2.47-2.520.31581650.26733229X-RAY DIFFRACTION99.85
2.52-2.580.2531520.25863213X-RAY DIFFRACTION99.91
2.58-2.640.2161680.25263235X-RAY DIFFRACTION99.91
2.64-2.710.2771920.24943206X-RAY DIFFRACTION99.91
2.71-2.790.28161820.24293224X-RAY DIFFRACTION99.82
2.79-2.880.2781580.24223264X-RAY DIFFRACTION99.94
2.88-2.990.26441640.25313229X-RAY DIFFRACTION99.82
2.99-3.110.25011740.24213215X-RAY DIFFRACTION99.76
3.11-3.250.25091420.23123256X-RAY DIFFRACTION99.91
3.25-3.420.23841680.22183233X-RAY DIFFRACTION99.68
3.42-3.630.2241610.19693250X-RAY DIFFRACTION99.85
3.63-3.910.22941880.20533239X-RAY DIFFRACTION99.85
3.91-4.310.19431670.18463245X-RAY DIFFRACTION99.74
4.31-4.930.20621830.18423238X-RAY DIFFRACTION99.97
4.93-6.210.2431540.21513290X-RAY DIFFRACTION99.91
6.21-42.040.21071930.20573267X-RAY DIFFRACTION99.28

+
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