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- PDB-1vzv: STRUCTURE OF VARICELLA-ZOSTER VIRUS PROTEASE -

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Basic information

Entry
Database: PDB / ID: 1vzv
TitleSTRUCTURE OF VARICELLA-ZOSTER VIRUS PROTEASE
ComponentsVARICELLA-ZOSTER VIRUS PROTEASE
KeywordsSERINE PROTEASE / HYDROLASE / VIRAL PROTEASE / VARICELLA-ZOSTER VIRUS / COAT PROTEIN
Function / homology
Function and homology information


assemblin / nuclear capsid assembly / viral release from host cell / host cell cytoplasm / serine-type endopeptidase activity / host cell nucleus / proteolysis / identical protein binding
Similarity search - Function
Serine Protease, Human Cytomegalovirus Protease; Chain A / Herpesvirus/Caudovirus protease domain / Peptidase S21 / Herpesvirus protease superfamily / Assemblin (Peptidase family S21) / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Capsid scaffolding protein
Similarity search - Component
Biological speciesHuman herpesvirus 3 (Varicella-zoster virus)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsQiu, X. / Jason, C.A. / Culp, J.S. / Richardson, S.B. / Debouck, C. / Smith, W.W. / Abdel-Meguid, S.S.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Crystal structure of varicella-zoster virus protease.
Authors: Qiu, X. / Janson, C.A. / Culp, J.S. / Richardson, S.B. / Debouck, C. / Smith, W.W. / Abdel-Meguid, S.S.
#1: Journal: Nature / Year: 1996
Title: Unique Fold and Active Site in Cytomegalovirus Protease
Authors: Qiu, X. / Culp, J.S. / Dilella, A.G. / Hellmig, B. / Hoog, S.S. / Janson, C.A. / Smith, W.W. / Abdel-Meguid, S.S.
History
DepositionFeb 10, 1997Processing site: BNL
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VARICELLA-ZOSTER VIRUS PROTEASE


Theoretical massNumber of molelcules
Total (without water)24,6551
Polymers24,6551
Non-polymers00
Water00
1
A: VARICELLA-ZOSTER VIRUS PROTEASE

A: VARICELLA-ZOSTER VIRUS PROTEASE


Theoretical massNumber of molelcules
Total (without water)49,3092
Polymers49,3092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+2/31
Buried area2600 Å2
ΔGint-17 kcal/mol
Surface area19080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)90.000, 90.000, 117.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein VARICELLA-ZOSTER VIRUS PROTEASE / ASSEMBLIN


Mass: 24654.525 Da / Num. of mol.: 1 / Fragment: RESIDUES 10 - 236 / Mutation: C10M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 3 (Varicella-zoster virus)
Genus: Varicellovirus / Strain: ACYCLOVIR-RESISTANT STRAIN 40A2 / Production host: Escherichia coli (E. coli)
References: UniProt: P09286, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 60 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 Mphosphate1reservoir
22.5 M1reservoirNaCl
310 mg/mlprotein1drop

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Dec 28, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 5419 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.07
Reflection
*PLUS
Highest resolution: 3 Å

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
XENGENdata scaling
X-PLORphasing
RefinementResolution: 3→7 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.223 -
obs0.223 4903
Displacement parametersBiso mean: 25 Å2
Refinement stepCycle: LAST / Resolution: 3→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1623 0 0 0 1623
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg25.1
X-RAY DIFFRACTIONx_improper_angle_deg1.8

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