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- PDB-2zug: Crystal structure of WSSV ICP11 -

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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
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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


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

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Experimental details

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Experiment

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

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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

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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

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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 %

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