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- PDB-1no7: Structure of the Large Protease Resistant Upper Domain of VP5, th... -

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Basic information

Entry
Database: PDB / ID: 1no7
TitleStructure of the Large Protease Resistant Upper Domain of VP5, the Major Capsid Protein of Herpes Simplex Virus-1
ComponentsMajor capsid protein
KeywordsVIRAL PROTEIN / novel fold / alpha plus beta / viral capsid protein / folding nucleus
Function / homologyT=16 icosahedral viral capsid / Herpesvirus major capsid protein / Herpesvirus major capsid protein, upper domain superfamily / Herpes virus major capsid protein / host cell nucleus / structural molecule activity / Major capsid protein
Function and homology information
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsBowman, B.R. / Baker, M.L. / Rixon, F.J. / Chiu, W. / Quiocho, F.A.
CitationJournal: Embo J. / Year: 2003
Title: Structure of the herpesvirus major capsid protein
Authors: Bowman, B.R. / Baker, M.L. / Rixon, F.J. / Chiu, W. / Quiocho, F.A.
History
DepositionJan 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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: Major capsid protein
B: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)130,3402
Polymers130,3402
Non-polymers00
Water00
1
A: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)65,1701
Polymers65,1701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)65,1701
Polymers65,1701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.072, 99.072, 454.684
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Major capsid protein / Capsid protein VP5


Mass: 65169.766 Da / Num. of mol.: 2 / Fragment: VP5 upper domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Genus: Simplexvirus / Gene: UL19 / Plasmid: pET32 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P06491

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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: 4.87 Å3/Da / Density % sol: 74.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: sodium acetate, imidazole, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1250 mM1dropNaCl
210 mMTris1droppH8.0
310 mMdithiothreitol1drop
420 mg/mlprotein1drop
50.8-1 Msodium acetate1reservoir
6100 mMimidizole1reservoirpH6.0-6.8

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-BM10.97885
SYNCHROTRONAPS 19-ID20.95679
Detector
TypeIDDetectorDate
CUSTOM-MADE1CCDDec 21, 2000
CUSTOM-MADE2CCDJan 1, 2001
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.978851
20.956791
ReflectionResolution: 2.9→50 Å / Num. obs: 47194 / % possible obs: 91.2 % / Biso Wilson estimate: 31 Å2 / Net I/σ(I): 7
Reflection shellHighest resolution: 2.9 Å / Mean I/σ(I) obs: 3.3 / % possible all: 80.4
Reflection
*PLUS
Num. measured all: 308549 / Rmerge(I) obs: 0.101
Reflection shell
*PLUS
% possible obs: 80.4 % / Rmerge(I) obs: 0.205

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.9→47.09 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 408294 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.289 4747 10.1 %RANDOM
Rwork0.255 ---
obs0.255 47193 91.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.194 Å2 / ksol: 0.291374 e/Å3
Displacement parametersBiso mean: 62.2 Å2
Baniso -1Baniso -2Baniso -3
1-13.67 Å20 Å20 Å2
2--13.67 Å20 Å2
3----27.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a1.11 Å1.02 Å
Refinement stepCycle: LAST / Resolution: 2.9→47.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8179 0 0 0 8179
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d1.28
X-RAY DIFFRACTIONc_mcbond_it11.471.5
X-RAY DIFFRACTIONc_mcangle_it17.82
X-RAY DIFFRACTIONc_scbond_it19.362
X-RAY DIFFRACTIONc_scangle_it26.042.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.419 674 9.8 %
Rwork0.415 6204 -
obs--81.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.254
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.28

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