[English] 日本語
Yorodumi
- PDB-8y30: Crystal structure of Staphylococcus aureus RecJ protein in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8y30
TitleCrystal structure of Staphylococcus aureus RecJ protein in complex with Mg2+
ComponentsSingle-stranded-DNA-specific exonuclease RecJ
KeywordsHYDROLASE / exonuclease / DNA repair
Function / homology
Function and homology information


5'-3' exonuclease activity / DNA recombination / nucleic acid binding / DNA repair
Similarity search - Function
Single-stranded-DNA-specific exonuclease RecJ, C-terminal / Single-strand DNA-specific exonuclease, C terminal domain / Bacterial RecJ exonuclease / RecJ, OB domain / RecJ OB domain / : / DDH domain / DHH family, N-terminal domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain
Similarity search - Domain/homology
Single-stranded-DNA-specific exonuclease RecJ
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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: To Be Published
Title: Structure of Staphylococcus aureus RecJ
Authors: Cheng, K. / Wang, Y.
History
DepositionJan 27, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Single-stranded-DNA-specific exonuclease RecJ
B: Single-stranded-DNA-specific exonuclease RecJ
C: Single-stranded-DNA-specific exonuclease RecJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,13618
Polymers257,1263
Non-polymers1,01015
Water99155
1
A: Single-stranded-DNA-specific exonuclease RecJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0456
Polymers85,7091
Non-polymers3375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Single-stranded-DNA-specific exonuclease RecJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0456
Polymers85,7091
Non-polymers3375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Single-stranded-DNA-specific exonuclease RecJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0456
Polymers85,7091
Non-polymers3375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)199.313, 199.313, 62.764
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

-
Components

#1: Protein Single-stranded-DNA-specific exonuclease RecJ


Mass: 85708.602 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: recJ, C7M54_09320, DD547_01719, EP54_09380, EQ90_02295, FAF17_07585, GO736_02485, GO814_13090, GO942_04975, GQX37_04600, HMPREF3211_01788, NCTC10702_02567, NCTC13131_01854, SAHC1335_02661, ...Gene: recJ, C7M54_09320, DD547_01719, EP54_09380, EQ90_02295, FAF17_07585, GO736_02485, GO814_13090, GO942_04975, GQX37_04600, HMPREF3211_01788, NCTC10702_02567, NCTC13131_01854, SAHC1335_02661, SAMEA103891415_01718, SAMEA2076235_02465, SAMEA2078260_02401, SAMEA2078588_02434, SAMEA2078837_02538, SAMEA2080344_02433, SAMEA2081063_02523, SAMEA4008575_02672
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D6HJB1
#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.: 9 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% peg 3350, 0.1 M (NH4)2SO4, 0.05 M MgSO4, pH 6.5

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.8→99.66 Å / Num. obs: 68089 / % possible obs: 98.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 71.88 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.6
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 9925

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata processing
autoPROCdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→31 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 32.0042
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2777 3492 5.13 %
Rwork0.2456 64546 -
obs0.2473 68038 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.4 Å2
Refinement stepCycle: LAST / Resolution: 2.8→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18036 0 51 55 18142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011118375
X-RAY DIFFRACTIONf_angle_d1.512824864
X-RAY DIFFRACTIONf_chiral_restr0.10052862
X-RAY DIFFRACTIONf_plane_restr0.02373207
X-RAY DIFFRACTIONf_dihedral_angle_d17.48366942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.840.43271330.34462550X-RAY DIFFRACTION96.34
2.84-2.880.35391020.33232597X-RAY DIFFRACTION98.18
2.88-2.920.32751060.32932619X-RAY DIFFRACTION100
2.92-2.970.36081290.32692565X-RAY DIFFRACTION97.61
2.97-3.010.3849940.34882603X-RAY DIFFRACTION97.58
3.01-3.070.33521160.34522624X-RAY DIFFRACTION100
3.07-3.120.36361900.34272543X-RAY DIFFRACTION98.52
3.12-3.180.38951120.32452575X-RAY DIFFRACTION98.53
3.18-3.250.30861180.31762618X-RAY DIFFRACTION100
3.25-3.320.34451470.30182618X-RAY DIFFRACTION97.67
3.32-3.390.34891140.29122569X-RAY DIFFRACTION100
3.39-3.480.3271500.30142604X-RAY DIFFRACTION98.64
3.48-3.570.31521840.28452520X-RAY DIFFRACTION99.52
3.57-3.680.32721580.27492631X-RAY DIFFRACTION99.25
3.68-3.80.30481940.27562486X-RAY DIFFRACTION99.26
3.8-3.930.31071410.26452595X-RAY DIFFRACTION98.59
3.93-4.090.29841260.2412619X-RAY DIFFRACTION99.89
4.09-4.270.29541520.2282563X-RAY DIFFRACTION98.8
4.27-4.50.25531510.22062577X-RAY DIFFRACTION99.27
4.5-4.780.23281170.21192600X-RAY DIFFRACTION99.74
4.78-5.150.21921190.21782611X-RAY DIFFRACTION99.2
5.15-5.660.30391730.25082579X-RAY DIFFRACTION99.49
5.66-6.480.26581710.25112532X-RAY DIFFRACTION98.87
6.48-8.130.20541470.20742585X-RAY DIFFRACTION99.31
8.14-310.18761480.15392563X-RAY DIFFRACTION98.05
Refinement TLS params.Method: refined / Origin x: 51.3153383578 Å / Origin y: -89.8050954504 Å / Origin z: 18.8229931527 Å
111213212223313233
T0.528866575482 Å2-0.0371090179743 Å2-0.00219465290773 Å2-0.511905483641 Å20.0340368681258 Å2--0.468006135893 Å2
L0.139283333934 °2-0.036621328827 °20.0912851654452 °2-0.233922425289 °2-0.0111062817992 °2--0.0482628645313 °2
S0.00680458317126 Å °-0.0391704794533 Å °0.0253314079641 Å °-0.0387966368753 Å °-0.0458892138662 Å °0.0155389611856 Å °-0.0211559604497 Å °-0.0418401282845 Å °0.0430101615172 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