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- PDB-2edm: Crystal Structure of Envelope Protein VP26 from White Spot Syndro... -

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Basic information

Entry
Database: PDB / ID: 2edm
TitleCrystal Structure of Envelope Protein VP26 from White Spot Syndrome Virus (WSSV)
Components22kDa structural protein VP22
KeywordsVIRAL PROTEIN / beta barrel / beta sheet protruding region
Function / homology
Function and homology information


WSSV envelope protein-like / White spot syndrome virus structural envelope protein Vp28 / WSSV envelope protein Vp28 superfamily / White spot syndrome virus structural envelope protein VP / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesShrimp white spot syndrome virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsHew, C.L. / Tang, X.H. / Sivaraman, J.
CitationJournal: J.Virol. / Year: 2007
Title: Crystal Structures of Major Envelope Proteins VP26 and VP28 from White Spot Syndrome Virus Shed Light on Their Evolutionary Relationship
Authors: Tang, X.H. / Wu, J.L. / Sivaraman, J. / Hew, C.L.
History
DepositionFeb 14, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 23, 2014Group: Other
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 22kDa structural protein VP22


Theoretical massNumber of molelcules
Total (without water)17,4481
Polymers17,4481
Non-polymers00
Water2,756153
1
A: 22kDa structural protein VP22

A: 22kDa structural protein VP22

A: 22kDa structural protein VP22


Theoretical massNumber of molelcules
Total (without water)52,3443
Polymers52,3443
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Unit cell
Length a, b, c (Å)73.915, 73.915, 199.313
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein 22kDa structural protein VP22 / Vp26 / Vp26 structural protein / WSSV367 / Major virion protein VP26 / ORF153 / VP26 / gene family ...Vp26 / Vp26 structural protein / WSSV367 / Major virion protein VP26 / ORF153 / VP26 / gene family 1 / Wsv311 / P22 / 26 kDa structural protein VP26


Mass: 17447.924 Da / Num. of mol.: 1 / Fragment: residues 41-201
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shrimp white spot syndrome virus / Genus: Whispovirus / Species: White spot syndrome virus 1 / Plasmid: pGEX6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: Q9ICG6, UniProt: Q0PW17*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 0.1M citric acid, 3.0M sodium chloride, 1% w/v polyethylene glycol 3350, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.9782, 0.9787, 0.9600
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 15, 2005
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97821
20.97871
30.961
ReflectionResolution: 2.2→50 Å / Num. obs: 10798 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 23 % / Rsym value: 0.09
Reflection shellResolution: 2.2→2.3 Å

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Processing

Software
NameClassification
HKL-2000data collection
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→39.3 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: ANOMALOUS DATA WAS USED IN THE REFINEMENT.
RfactorNum. reflectionSelection details
Rfree0.278 2061 RANDOM
Rwork0.217 --
all0.278 --
obs0.217 10798 -
Refinement stepCycle: LAST / Resolution: 2.2→39.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 0 153 1365
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0074
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.22
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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