[English] 日本語
Yorodumi
- PDB-9ku2: Structure of taterapox core protease central domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ku2
TitleStructure of taterapox core protease central domain
ComponentsViral core cysteine proteinase
KeywordsVIRAL PROTEIN / orthopoxvirus / mpox / protease
Function / homologyPeptidase C57, Vaccinia virus protein I7 / Vaccinia virus I7 processing peptidase / cysteine-type peptidase activity / Papain-like cysteine peptidase superfamily / virion component / proteolysis / Viral core cysteine proteinase
Function and homology information
Biological speciesTaterapox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.895 Å
AuthorsLi, D. / Wang, H. / Ji, X. / Gao, Y. / Wang, W. / Yang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81902063 China
CitationJournal: To Be Published
Title: Structure of taterapox core protease central domain
Authors: Li, D. / Wang, H. / Ji, X. / Gao, Y. / Wang, W. / Yang, H.
History
DepositionDec 3, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Viral core cysteine proteinase


Theoretical massNumber of molelcules
Total (without water)49,4201
Polymers49,4201
Non-polymers00
Water4,414245
1
A: Viral core cysteine proteinase

A: Viral core cysteine proteinase


Theoretical massNumber of molelcules
Total (without water)98,8402
Polymers98,8402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area1910 Å2
ΔGint-16 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.900, 65.677, 95.881
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein Viral core cysteine proteinase


Mass: 49419.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Due to natural protein degradation, the molecular weight of the crystallised piece of protein is 23517 Da.
Source: (gene. exp.) Taterapox virus / Gene: TATV_DAH68_079 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0NPD2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium citrate, pH 5.5 and 15% w/v PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97853 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.895→47.94 Å / Num. obs: 38629 / % possible obs: 99.9 % / Redundancy: 11.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.166 / Rrim(I) all: 0.174 / Net I/σ(I): 11.41
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.9-2.010.82532760.8720.8631
2.01-2.150.57230720.9370.5981
2.15-2.320.39428970.9650.4121
2.32-2.540.28326650.9850.2961
2.54-2.840.20924440.9890.2191
2.84-3.280.13621480.9950.1431
3.28-4.010.09618560.9970.1011
4.01-5.650.07714660.9970.0811
5.65-47.940.0728680.9970.0761

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.895→36.84 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1885 3742 9.69 %
Rwork0.1466 --
obs0.1507 38622 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.895→36.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1645 0 0 250 1895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191693
X-RAY DIFFRACTIONf_angle_d1.3542278
X-RAY DIFFRACTIONf_dihedral_angle_d11.784980
X-RAY DIFFRACTIONf_chiral_restr0.097236
X-RAY DIFFRACTIONf_plane_restr0.009287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8951-1.91910.29991380.24211290X-RAY DIFFRACTION99
1.9191-1.94440.27731370.23121241X-RAY DIFFRACTION100
1.9444-1.9710.21871420.19771316X-RAY DIFFRACTION100
1.971-1.99910.25311440.18131308X-RAY DIFFRACTION100
1.9991-2.0290.2221340.18621270X-RAY DIFFRACTION100
2.029-2.06070.22881360.17751298X-RAY DIFFRACTION100
2.0607-2.09450.19451400.17291296X-RAY DIFFRACTION100
2.0945-2.13060.22541410.15641295X-RAY DIFFRACTION100
2.1306-2.16930.19021350.1621292X-RAY DIFFRACTION100
2.1693-2.2110.19751370.15491295X-RAY DIFFRACTION100
2.211-2.25620.22571440.16081304X-RAY DIFFRACTION100
2.2562-2.30520.18371350.15241263X-RAY DIFFRACTION100
2.3052-2.35880.19061390.15581336X-RAY DIFFRACTION100
2.3588-2.41780.19761340.14691278X-RAY DIFFRACTION100
2.4178-2.48320.23781420.14491302X-RAY DIFFRACTION100
2.4832-2.55620.18931410.1541271X-RAY DIFFRACTION100
2.5562-2.63870.19871360.14611288X-RAY DIFFRACTION100
2.6387-2.7330.18261440.13921309X-RAY DIFFRACTION100
2.733-2.84240.17951390.13951314X-RAY DIFFRACTION100
2.8424-2.97170.21161350.12691275X-RAY DIFFRACTION100
2.9717-3.12830.17841370.13131297X-RAY DIFFRACTION100
3.1283-3.32420.1781390.12541305X-RAY DIFFRACTION100
3.3242-3.58060.1631350.13011275X-RAY DIFFRACTION100
3.5806-3.94060.14181390.12281285X-RAY DIFFRACTION100
3.9406-4.50990.16351420.11011310X-RAY DIFFRACTION100
4.5099-5.67870.16431370.14051288X-RAY DIFFRACTION100
5.6787-36.840.19521400.1841279X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 6.0906 Å / Origin y: -0.112 Å / Origin z: 30.3616 Å
111213212223313233
T0.132 Å20.0071 Å2-0.0099 Å2-0.1342 Å20.0055 Å2--0.1355 Å2
L1.2276 °20.0638 °2-0.3151 °2-1.4667 °20.0777 °2--1.555 °2
S-0.0125 Å °0.0007 Å °-0.0392 Å °0.0353 Å °-0.0084 Å °-0.0896 Å °0.0915 Å °0.0075 Å °0.0207 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