[English] 日本語
Yorodumi
- PDB-6ljo: African swine fever virus dUTPase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ljo
TitleAfrican swine fever virus dUTPase
ComponentsE165R
KeywordsVIRAL PROTEIN / ASFV / dUTPase / aDUT
Function / homology
Function and homology information


dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / virion component / host cell cytoplasm / metal ion binding
Similarity search - Function
dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily
Similarity search - Domain/homology
Deoxyuridine 5'-triphosphate nucleotidohydrolase / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesAfrican swine fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.28 Å
AuthorsLiang, R. / Peng, G.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31722056 China
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural comparisons of host and African swine fever virus dUTPases reveal new clues for inhibitor development.
Authors: Liang, R. / Wang, G. / Zhang, D. / Ye, G. / Li, M. / Shi, Y. / Shi, J. / Chen, H. / Peng, G.
History
DepositionDec 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: 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
Revision 1.2Jul 21, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E165R


Theoretical massNumber of molelcules
Total (without water)18,2851
Polymers18,2851
Non-polymers00
Water25214
1
A: E165R

A: E165R

A: E165R


Theoretical massNumber of molelcules
Total (without water)54,8563
Polymers54,8563
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area4690 Å2
ΔGint-32 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.014, 98.014, 98.014
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-209-

HOH

-
Components

#1: Protein E165R / E165R CDS protein


Mass: 18285.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus
Gene: E165R CDS, E165R, ASFV-Georgia_4-154, ASFV_Kyiv_2016_131_00207
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2X0SE53, UniProt: Q65199*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.15 Å3/Da / Density % sol: 42.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: 0.5M NaH2PO4/K2HPO4,PH 6.9

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 7330 / % possible obs: 100 % / Redundancy: 3.87 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.014 / Rrim(I) all: 0.087 / Χ2: 0.977 / Net I/av σ(I): 100.8 / Net I/σ(I): 1.74
Reflection shellResolution: 2.28→2.32 Å / Redundancy: 3.69 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 2.14 / Num. unique obs: 371 / CC1/2: 0.777 / CC star: 0.935 / Rpim(I) all: 0.682 / Rrim(I) all: 0.695 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.28→49.06 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.898 / SU B: 9.525 / SU ML: 0.223 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.374 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2735 374 5.1 %RANDOM
Rwork0.2282 ---
obs0.2307 6926 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.46 Å2 / Biso mean: 33.171 Å2 / Biso min: 11.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.28→49.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1139 0 0 14 1153
Biso mean---26.57 -
Num. residues----146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131163
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171125
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.6331578
X-RAY DIFFRACTIONr_angle_other_deg1.211.5712616
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.98715207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.015155
X-RAY DIFFRACTIONr_chiral_restr0.0670.2157
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021269
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02218
LS refinement shellResolution: 2.28→2.338 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.486 37 -
Rwork0.326 481 -
obs--97 %

+
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