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- PDB-5vyl: Crystal Structure of N-terminal half of Herpes Simplex virus Type... -

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Basic information

Entry
Database: PDB / ID: 5vyl
TitleCrystal Structure of N-terminal half of Herpes Simplex virus Type 1 UL37 protein
ComponentsInner tegument protein
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


microtubule-dependent intracellular transport of viral material towards cell periphery / protein-glutamine glutaminase activity / protein-glutamine glutaminase / viral tegument / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / virion assembly / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / host cell Golgi apparatus / host cell nucleus / identical protein binding
Similarity search - Function
Inner tegument protein / Herpesvirus UL37 / Herpesvirus UL37 tegument protein
Similarity search - Domain/homology
Inner tegument protein
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.51 Å
AuthorsKoenigsberg, A. / Heldwein, E.E.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI056346 United States
Burroughs Wellcome FundInvestigators in the Pathogenesis of Infectious Disease United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32 AI007422 United States
CitationJournal: J. Virol. / Year: 2017
Title: Crystal Structure of the N-Terminal Half of the Traffic Controller UL37 from Herpes Simplex Virus 1.
Authors: Koenigsberg, A.L. / Heldwein, E.E.
History
DepositionMay 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 11, 2017Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Inner tegument protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8232
Polymers61,8001
Non-polymers231
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-11 kcal/mol
Surface area22390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.232, 138.232, 164.220
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 Inner tegument protein


Mass: 61799.551 Da / Num. of mol.: 1 / Fragment: residues 1-575
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (strain 17) / Strain: 17 / Gene: UL37 / Plasmid: pET24
Details (production host): N-terminal His-SUMO tag cleavable by HRV3C protease
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): LOBSTR / References: UniProt: P10221
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.66 Å3/Da / Density % sol: 66.43 % / Description: Needles
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.1M Bicine pH 9.0, 8% PEG 20K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.51→164.22 Å / Num. obs: 12161 / % possible obs: 100 % / Redundancy: 14 % / Biso Wilson estimate: 97.01 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.441 / Rpim(I) all: 0.119 / Net I/σ(I): 8.7
Reflection shellResolution: 3.51→3.85 Å / Redundancy: 14.1 % / Rmerge(I) obs: 1.993 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2818 / CC1/2: 0.58 / Rpim(I) all: 0.539 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4k70

4k70


Resolution: 3.51→96.737 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.04
RfactorNum. reflection% reflectionSelection details
Rfree0.2816 1212 10.01 %Random selection
Rwork0.2401 ---
obs0.2442 12107 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 91.25 Å2
Refinement stepCycle: LAST / Resolution: 3.51→96.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3804 0 1 1 3806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063887
X-RAY DIFFRACTIONf_angle_d0.9335308
X-RAY DIFFRACTIONf_dihedral_angle_d4.992338
X-RAY DIFFRACTIONf_chiral_restr0.046633
X-RAY DIFFRACTIONf_plane_restr0.008685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5101-3.65060.43681300.35961176X-RAY DIFFRACTION100
3.6506-3.81680.32521310.31871173X-RAY DIFFRACTION100
3.8168-4.0180.33871300.30351175X-RAY DIFFRACTION100
4.018-4.26980.29771330.25711196X-RAY DIFFRACTION100
4.2698-4.59940.2441340.2081197X-RAY DIFFRACTION100
4.5994-5.06230.23881320.20171189X-RAY DIFFRACTION100
5.0623-5.79470.28521360.24631223X-RAY DIFFRACTION100
5.7947-7.30040.30421380.26481238X-RAY DIFFRACTION100
7.3004-96.7740.24021480.18821328X-RAY DIFFRACTION100

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