[English] 日本語
Yorodumi
- PDB-2zug: Crystal structure of WSSV ICP11 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2zug
TitleCrystal structure of WSSV ICP11
ComponentsORF115 (WSSV285) (Wsv230)
KeywordsVIRAL PROTEIN / DNA mimic protein / dimer / White spot syndrome virus
Function / homologyVP9 protein domain / White spot syndrome virus (WSSV), Orf116/126, N-terminal / VP9, N-terminal domain superfamily / VP9 protein / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / ICP11/P9
Function and homology information
Biological speciesShrimp white spot syndrome virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.72 Å
AuthorsWang, A.H.-J. / Wang, H.-C. / Ko, T.-P. / Lo, C.-F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: White spot syndrome virus protein ICP11: A histone-binding DNA mimic that disrupts nucleosome assembly
Authors: Wang, H.-C. / Wang, H.-C. / Ko, T.-P. / Lee, Y.-M. / Leu, J.-H. / Ho, C.-H. / Huang, W.-P. / Lo, C.-F. / Wang, A.H.-J.
History
DepositionOct 17, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ORF115 (WSSV285) (Wsv230)
B: ORF115 (WSSV285) (Wsv230)


Theoretical massNumber of molelcules
Total (without water)20,9542
Polymers20,9542
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-12 kcal/mol
Surface area8680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.595, 91.595, 98.352
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-97-

HOH

21B-99-

HOH

31B-108-

HOH

-
Components

#1: Protein ORF115 (WSSV285) (Wsv230) / ICP11


Mass: 10477.116 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shrimp white spot syndrome virus / Strain: Taiwan isolate / Gene: white spot syndrome virus / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q91LD0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 4.92 Å3/Da / Density % sol: 75.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M sodium acetate trihydrate, 2.2M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSRRC BL13B110.9762
SYNCHROTRONNSRRC BL13B120.9790, 0.9788, 0.9636
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJul 1, 2006
ADSC QUANTUM 3152CCDJul 1, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97621
20.9791
30.97881
40.96361
ReflectionResolution: 2.72→30 Å / Num. all: 11756 / Num. obs: 11437 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 9.4 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 30.3
Reflection shellResolution: 2.72→2.82 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1158 / % possible all: 88.2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.72→29.25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 569 -RANDOM
Rwork0.226 ---
all0.227 11756 --
obs0.227 10822 92.1 %-
Displacement parametersBiso mean: 66.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 2.72→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1243 0 0 39 1282
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_bond_d0.015
LS refinement shellResolution: 2.72→2.82 Å / Rfactor Rfree error: 0.035
RfactorNum. reflection% reflection
Rfree0.372 50 -
Rwork0.407 --
obs-854 74.2 %

+
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