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- PDB-16vp: CONSERVED CORE OF THE HERPES SIMPLEX VIRUS TRANSCRIPTIONAL REGULA... -

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Basic information

Entry
Database: PDB / ID: 16vp
TitleCONSERVED CORE OF THE HERPES SIMPLEX VIRUS TRANSCRIPTIONAL REGULATORY PROTEIN VP16
ComponentsPROTEIN (VP16, VMW65, ATIF)
KeywordsTRANSCRIPTIONAL REGULATORY PROTEIN
Function / homology
Function and homology information


replication compartment / regulation of viral transcription / DNA-templated viral transcription / viral tegument / biological process involved in interaction with host / host cell cytoplasmic vesicle / core promoter sequence-specific DNA binding / molecular function activator activity / protein-containing complex assembly / DNA-binding transcription factor binding ...replication compartment / regulation of viral transcription / DNA-templated viral transcription / viral tegument / biological process involved in interaction with host / host cell cytoplasmic vesicle / core promoter sequence-specific DNA binding / molecular function activator activity / protein-containing complex assembly / DNA-binding transcription factor binding / transcription regulator complex / structural constituent of virion / transcription coactivator activity / host cell cytoplasm / host cell perinuclear region of cytoplasm / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / host cell nucleus / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding
Similarity search - Function
Conserved core of transcriptional regulatory protein vp16 / Alpha trans-inducing (Alpha-TIF) / Alpha trans-inducing protein (Alpha-TIF) / Herpes simplex virus, Tegument protein VP16, C-terminal / Alpha trans-inducing (Alpha-TIF) superfamily / Alpha trans-inducing protein (Alpha-TIF) / Herpes simplex virus virion protein 16 C terminal / Alpha trans-inducing protein (Alpha-TIF) / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Tegument protein VP16
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.1 Å
AuthorsLiu, Y. / Gong, W. / Huang, C.C. / Herr, W. / Cheng, X.
CitationJournal: Genes Dev. / Year: 1999
Title: Crystal structure of the conserved core of the herpes simplex virus transcriptional regulatory protein VP16.
Authors: Liu, Y. / Gong, W. / Huang, C.C. / Herr, W. / Cheng, X.
History
DepositionFeb 11, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 28, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (VP16, VMW65, ATIF)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6723
Polymers41,4801
Non-polymers1922
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.500, 77.100, 84.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN (VP16, VMW65, ATIF)


Mass: 41480.227 Da / Num. of mol.: 1 / Fragment: CONSERVED CORE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Genus: Simplexvirus / Strain: STRAIN 17 / Production host: Escherichia coli (E. coli) / References: UniProt: P06492
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 7

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growpH: 4 / Details: pH 4.0
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %(w/v)PEG80001reservoir
250 mMpotassium phosphate1reservoir
310 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1
DetectorDetector: RAXIS AND MAR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 21163 / % possible obs: 96.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.3
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 2.8 / % possible all: 92.9
Reflection shell
*PLUS
% possible obs: 92.9 % / Num. unique obs: 1008

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Processing

Software
NameClassification
PHASESphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.1→7 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1427 7.3 %RANDOM
Rwork0.192 ---
obs-19677 92.9 %-
Displacement parametersBiso mean: 20 Å2
Refinement stepCycle: LAST / Resolution: 2.1→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2458 0 10 170 2638
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
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
LS refinement shellResolution: 2.1→2.19 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.32 173 7.6 %
Rwork0.255 2089 -
obs--86.5 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 7 Å / σ(F): 0 / % reflection Rfree: 7.3 % / Rfactor obs: 0.192 / Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4
LS refinement shell
*PLUS
Highest resolution: 2.1 Å / Rfactor Rfree: 0.32 / % reflection Rfree: 7.6 % / Rfactor Rwork: 0.255 / Num. reflection obs: 2262 / Rfactor obs: 0.255

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