[English] 日本語
Yorodumi
- PDB-5hlj: Crystal Structure of Major Envelope Protein VP24 from White Spot ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hlj
TitleCrystal Structure of Major Envelope Protein VP24 from White Spot Syndrome Virus
ComponentsVP24
KeywordsVIRAL PROTEIN / WSSV / VP24 / envelope protein
Function / homologyWhite spot syndrome virus structural envelope protein Vp28 / WSSV envelope protein Vp28 superfamily / White spot syndrome virus structural envelope protein VP / membrane => GO:0016020 / VP24
Function and homology information
Biological speciesWhite spot syndrome virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.406 Å
AuthorsSun, L.F. / Su, Y.T. / Zhao, Y.H. / Fu, Z.Q. / Wu, Y.K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31302225 China
CitationJournal: Sci Rep / Year: 2016
Title: Crystal Structure of Major Envelope Protein VP24 from White Spot Syndrome Virus
Authors: Sun, L.F. / Su, Y.T. / Zhao, Y.H. / Fu, Z.Q. / Wu, Y.K.
History
DepositionJan 15, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VP24


Theoretical massNumber of molelcules
Total (without water)21,2561
Polymers21,2561
Non-polymers00
Water97354
1
A: VP24

A: VP24

A: VP24


Theoretical massNumber of molelcules
Total (without water)63,7683
Polymers63,7683
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area7110 Å2
ΔGint-28 kcal/mol
Surface area21100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.735, 139.735, 139.735
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

-
Components

#1: Protein VP24


Mass: 21255.947 Da / Num. of mol.: 1 / Fragment: UNP residues 30-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) White spot syndrome virus / Plasmid: pET-21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q80BF2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 5.35 Å3/Da / Density % sol: 77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris-HCl, pH 8.5, 2.75 M NH4AC

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. obs: 17758 / % possible obs: 99.9 % / Redundancy: 20.6 % / Biso Wilson estimate: 71.49 Å2 / Rmerge(I) obs: 0.074 / Net I/av σ(I): 51.361 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
2.4-2.4420.41100
2.44-2.4922.11100
2.49-2.5322.21100
2.53-2.5922.41100
2.59-2.6422.31100
2.64-2.722.311000.847
2.7-2.7722.311000.72
2.77-2.8522.311000.519
2.85-2.9322.411000.376
2.93-3.0222.111000.278
3.02-3.132211000.207
3.13-3.2621.611000.15
3.26-3.4121.111000.119
3.41-3.5920.411000.096
3.59-3.8119.311000.08
3.81-4.118.611000.068
4.1-4.5217.1199.80.059
4.52-5.1716.611000.054
5.17-6.5117.911000.052
6.51-10018198.80.043

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
SCALEPACKdata reduction
PHENIXphasing
RefinementStarting model: SAD

Resolution: 2.406→31.246 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.15 / Stereochemistry target values: ML
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflectionSelection details
Rfree0.1926 1760 9.93 %Random
Rwork0.1708 ---
obs0.173 17728 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.406→31.246 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1328 0 0 54 1382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081350
X-RAY DIFFRACTIONf_angle_d1.1251824
X-RAY DIFFRACTIONf_dihedral_angle_d13.688497
X-RAY DIFFRACTIONf_chiral_restr0.044207
X-RAY DIFFRACTIONf_plane_restr0.004238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4064-2.47140.29021360.30181213X-RAY DIFFRACTION100
2.4714-2.54410.34581330.27581213X-RAY DIFFRACTION100
2.5441-2.62620.29731380.26471220X-RAY DIFFRACTION100
2.6262-2.720.2721360.24241207X-RAY DIFFRACTION100
2.72-2.82880.24971300.23891223X-RAY DIFFRACTION100
2.8288-2.95750.25541320.22891217X-RAY DIFFRACTION100
2.9575-3.11330.2451390.21011219X-RAY DIFFRACTION100
3.1133-3.30810.22721360.20191216X-RAY DIFFRACTION100
3.3081-3.56320.20351390.18581252X-RAY DIFFRACTION100
3.5632-3.92120.19821310.17621221X-RAY DIFFRACTION100
3.9212-4.48710.15861380.15151236X-RAY DIFFRACTION100
4.4871-5.64790.13841350.1351244X-RAY DIFFRACTION100
5.6479-31.24830.18971370.14361287X-RAY DIFFRACTION99

+
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