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- PDB-2f5u: Structural Characterization of the UL25 DNA Packaging Protein fro... -

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Basic information

Entry
Database: PDB / ID: 2f5u
TitleStructural Characterization of the UL25 DNA Packaging Protein from Herpes Simplex Virus Type 1
ComponentsVirion protein UL25
KeywordsVIRAL PROTEIN / HSV-1 / Capsid Protein / DNA packaging / UL25 / Head Completion
Function / homologyHerpesvirus UL25 / Herpesvirus UL25 family / viral genome packaging / viral penetration into host nucleus / viral capsid / host cell / symbiont entry into host cell / host cell nucleus / Capsid vertex component 2
Function and homology information
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsBowman, B.R.
CitationJournal: J.Virol. / Year: 2006
Title: Structural characterization of the UL25 DNA-packaging protein from herpes simplex virus type 1
Authors: Bowman, B.R. / Welschhans, R.L. / Jayaram, H. / Stow, N.D. / Preston, V.G. / Quiocho, F.A.
History
DepositionNov 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 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: Virion protein UL25


Theoretical massNumber of molelcules
Total (without water)48,4341
Polymers48,4341
Non-polymers00
Water3,387188
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.600, 67.600, 119.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailspossible monomer

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Components

#1: Protein Virion protein UL25


Mass: 48433.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Genus: Simplexvirus / Gene: UL25 / Production host: Escherichia coli (E. coli) / References: UniProt: P10209
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.19 Å3/Da / Density % sol: 43.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15-25% PEG MME 2000, 200mM Triethylamine N-oxide hydrate, 100mM Tris pH 8.0 to 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: .97948, .97937
DetectorType: SBC-2 / Detector: CCD / Date: Jun 24, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979481
20.979371
ReflectionResolution: 2.1→50 Å / Num. all: 191657 / Num. obs: 191657 / % possible obs: 97.9 % / Observed criterion σ(I): 2.5 / Biso Wilson estimate: 14.1 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→34.1 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1958343.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2527 9.9 %RANDOM
Rwork0.227 ---
all0.227 25583 --
obs0.227 25583 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.3781 Å2 / ksol: 0.344785 e/Å3
Displacement parametersBiso mean: 32.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20 Å20 Å2
2--4.81 Å20 Å2
3----5.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.1→34.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3149 0 0 188 3337
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.951.5
X-RAY DIFFRACTIONc_mcangle_it3.392
X-RAY DIFFRACTIONc_scbond_it2.622
X-RAY DIFFRACTIONc_scangle_it3.872.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 399 9.6 %
Rwork0.248 3766 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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