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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8zef
TitleCrystal structure of Staphylococcus aureus DinG protein in complex with ssDNA and Ca2+
Components
  • 3'-5' exonuclease DinG
  • DNA (5'-D(*TP*TP*TP*TP*TP*TP*T)-3')
  • DNA (5'-D(P*TP*TP*TP*T)-3')
KeywordsHYDROLASE/DNA / exonuclease / DNA repair / HYDROLASE-DNA complex
Function / homology
Function and homology information


hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / DNA replication proofreading / 3'-5' exonuclease activity / helicase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / DNA binding / ATP binding / cytosol
Similarity search - Function
3'-5' exonuclease DinG / DNA polymerase III epsilon subunit, exonuclease domain / Exonuclease / HELICc2 / ATP-dependent helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / Exonuclease, RNase T/DNA polymerase III / EXOIII ...3'-5' exonuclease DinG / DNA polymerase III epsilon subunit, exonuclease domain / Exonuclease / HELICc2 / ATP-dependent helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / Exonuclease, RNase T/DNA polymerase III / EXOIII / Superfamilies 1 and 2 helicase C-terminal domain profile. / Ribonuclease H superfamily / Ribonuclease H-like superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / 3'-5' exonuclease DinG
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
chemical production metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsCheng, K. / Gao, T. / Hao, W.
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 DinG
Authors: Cheng, K. / Gao, T. / Hao, W.
History
DepositionMay 6, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3'-5' exonuclease DinG
B: DNA (5'-D(P*TP*TP*TP*T)-3')
C: DNA (5'-D(*TP*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8125
Polymers107,7323
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-57 kcal/mol
Surface area42350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.855, 128.045, 302.999
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein 3'-5' exonuclease DinG


Mass: 104475.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria)
Gene: dinG, SAOUHSC_01472 / Production host: Escherichia coli (E. coli)
References: UniProt: Q2FYH5, Hydrolases; Acting on ester bonds
#2: DNA chain DNA (5'-D(P*TP*TP*TP*T)-3')


Mass: 1171.814 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) chemical production metagenome (others)
#3: DNA chain DNA (5'-D(*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 2084.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) chemical production metagenome (others)
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 5% v/v Tacsimate (pH 7.0), 0.1 M HEPES (pH 7.0), 8% w/v Polyethylene glycol monomethyl ether 5,000 and 50 mM CaCl2.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.21→39.65 Å / Num. obs: 22275 / % possible obs: 99.58 % / Redundancy: 6 % / Biso Wilson estimate: 111.43 Å2 / Rmerge(I) obs: 0.102 / Net I/av σ(I): 17.3 / Net I/σ(I): 2.43
Reflection shellResolution: 3.21→3.33 Å / Rmerge(I) obs: 1.514 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3207

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.21→39.65 Å / SU ML: 0.5115 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.3298
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2917 1106 4.97 %
Rwork0.2833 21169 -
obs0.2836 22275 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 154.64 Å2
Refinement stepCycle: LAST / Resolution: 3.21→39.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7280 216 2 0 7498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817657
X-RAY DIFFRACTIONf_angle_d1.154810369
X-RAY DIFFRACTIONf_chiral_restr0.0871169
X-RAY DIFFRACTIONf_plane_restr0.01241282
X-RAY DIFFRACTIONf_dihedral_angle_d11.73521054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.21-3.360.4731410.42112602X-RAY DIFFRACTION99.6
3.36-3.540.39221240.37252612X-RAY DIFFRACTION99.49
3.54-3.760.35931330.34682600X-RAY DIFFRACTION99.49
3.76-4.050.3441430.34162656X-RAY DIFFRACTION99.61
4.05-4.450.33061260.29262598X-RAY DIFFRACTION99.53
4.45-5.10.30681530.26682651X-RAY DIFFRACTION99.93
5.1-6.420.29851410.30742668X-RAY DIFFRACTION99.82
6.42-39.650.21611450.22552782X-RAY DIFFRACTION99.22
Refinement TLS params.Method: refined / Origin x: 43.4539309831 Å / Origin y: -5.58812741543 Å / Origin z: 38.4348454159 Å
111213212223313233
T0.898517691439 Å2-0.0811774448144 Å2-0.13157171614 Å2-1.1241300014 Å20.186632786639 Å2--0.901358283128 Å2
L1.41359412621 °2-0.112041866488 °2-0.087657207426 °2-1.06207496819 °20.0412183502652 °2--1.53843827346 °2
S-0.0387384474461 Å °-0.711900959895 Å °-0.0509431013664 Å °0.503933377744 Å °-0.00384941880686 Å °-0.309157628481 Å °-0.184739558248 Å °0.263049271444 Å °0.0728031498405 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