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- PDB-4xal: Crystal structure of the conserved core domain of VP22 from HSV-1 -

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Basic information

Entry
Database: PDB / ID: 4xal
TitleCrystal structure of the conserved core domain of VP22 from HSV-1
Components
  • Tegument protein VP22
  • peptide SSGVDL
KeywordsVIRAL PROTEIN / VP22 / HSV-1 / MHV-68 / ORF52
Function / homologyHerpesvirus UL49 tegument protein / Herpesvirus UL49 tegument protein / viral tegument / host cell Golgi apparatus / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response / host cell nucleus / Tegument protein VP22
Function and homology information
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / molecular replacement / Resolution: 1.869 Å
AuthorsHew, K. / Dahlroth, S.L. / Nordlund, P.
CitationJournal: J.Gen.Virol. / Year: 2015
Title: VP22 core domain from Herpes simplex virus 1 reveals a surprising structural conservation in both the Alpha- and Gammaherpesvirinae subfamilies.
Authors: Hew, K. / Dahlroth, S.L. / Pan, L.X. / Cornvik, T. / Nordlund, P.
History
DepositionDec 15, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tegument protein VP22
B: peptide SSGVDL


Theoretical massNumber of molelcules
Total (without water)15,1352
Polymers15,1352
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-1 kcal/mol
Surface area7450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.940, 64.940, 107.645
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Tegument protein VP22


Mass: 14558.493 Da / Num. of mol.: 1 / Fragment: core domain (UNP RESIDUES 174-281)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (strain 17) / Strain: 17 / Gene: UL49 / Production host: Escherichia coli (E. coli) / References: UniProt: P10233
#2: Protein/peptide peptide SSGVDL


Mass: 576.599 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (strain 17) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.16 Å3/Da / Density % sol: 43.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 40% PEG 300 and 0.1 M Phosphate citrate pH 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.9762 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.87→30 Å / Num. obs: 11585 / % possible obs: 98.7 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.052 / Χ2: 1.036 / Net I/av σ(I): 41.175 / Net I/σ(I): 16.5 / Num. measured all: 119894
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.87-1.9410.50.28911330.98999.8
1.94-2.0110.60.18511271.04999.8
2.01-2.1110.50.13211401.11199.8
2.11-2.2210.60.10111321.10199.5
2.22-2.3610.50.07211531.06199.5
2.36-2.5410.50.0611391.05799.2
2.54-2.7910.50.04511621.02699
2.79-3.210.40.04311610.96298.3
3.2-4.039.80.05511851.04697.5
4.03-309.50.02912530.95895.4

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Phasing

Phasing
Method
SIRAS
molecular replacement
Phasing dmFOM : 0.63 / FOM acentric: 0.63 / FOM centric: 0.65 / Reflection: 11584 / Reflection acentric: 9320 / Reflection centric: 2264

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
PHASER2.5.6phasing
PHENIXphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SIRAS / Resolution: 1.869→24.923 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2511 580 5.01 %
Rwork0.2084 --
obs0.2105 11582 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.869→24.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms743 0 0 74 817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007768
X-RAY DIFFRACTIONf_angle_d0.9641041
X-RAY DIFFRACTIONf_dihedral_angle_d13.158290
X-RAY DIFFRACTIONf_chiral_restr0.04118
X-RAY DIFFRACTIONf_plane_restr0.006137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8694-2.05740.27511410.21972683X-RAY DIFFRACTION100
2.0574-2.35490.2341430.20162715X-RAY DIFFRACTION100
2.3549-2.96620.23971440.21462745X-RAY DIFFRACTION99
2.9662-24.92550.25781520.20542859X-RAY DIFFRACTION98

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