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- PDB-4tt0: Crystal structure of fragment 1600-1733 of HSV1 UL36 in the prese... -

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Basic information

Entry
Database: PDB / ID: 4tt0
TitleCrystal structure of fragment 1600-1733 of HSV1 UL36 in the presence of 1M potassium iodide
ComponentsDeneddylase
KeywordsHYDROLASE / Fibrous protein Tegument protein
Function / homology
Function and homology information


nuclear capsid assembly / deNEDDylase activity / symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / viral tegument / deubiquitinase activity / viral DNA genome replication / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / host cell cytoplasm / cysteine-type deubiquitinase activity ...nuclear capsid assembly / deNEDDylase activity / symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / viral tegument / deubiquitinase activity / viral DNA genome replication / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / host cell cytoplasm / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / host cell nucleus / proteolysis
Similarity search - Function
Herpesvirus large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Large tegument protein deneddylase / Herpesvirus tegument ubiquitin-specific protease (htUSP) domain profile. / Herpesvirus large tegument protein, USP domain / Herpesvirus tegument protein, N-terminal conserved region / : / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
IODIDE ION / Large tegument protein deneddylase
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.599 Å
AuthorsScrima, N. / Bressanelli, S. / Roche, S.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Insights into Herpesvirus Tegument Organization from Structural Analyses of the 970 Central Residues of HSV-1 UL36 Protein.
Authors: Scrima, N. / Lepault, J. / Boulard, Y. / Pasdeloup, D. / Bressanelli, S. / Roche, S.
History
DepositionJun 19, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3May 8, 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: Deneddylase
B: Deneddylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,26242
Polymers30,1862
Non-polymers5,07640
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9590 Å2
ΔGint-47 kcal/mol
Surface area17900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.939, 110.939, 154.930
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 Deneddylase / Tegument protein VP1-2 / Tegument protein VP1/2 / HSV1 UL36


Mass: 15093.057 Da / Num. of mol.: 2 / Fragment: Residues 1625-1757
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1(type 1 / strain 17)
Production host: Escherichia coli (E. coli)
References: UniProt: P10220, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.56 Å3/Da / Density % sol: 73.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM Hepes, 2M ammonium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.90745 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.90745 Å / Relative weight: 1
ReflectionResolution: 2.599→48.038 Å / Num. obs: 32816 / % possible obs: 100 % / Redundancy: 6.4 % / Net I/σ(I): 14.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.599→48.038 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 23.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.242 911 5.07 %Random selection
Rwork0.1879 ---
obs0.1905 17954 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.599→48.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1985 0 40 31 2056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082002
X-RAY DIFFRACTIONf_angle_d1.0312707
X-RAY DIFFRACTIONf_dihedral_angle_d14.53759
X-RAY DIFFRACTIONf_chiral_restr0.044323
X-RAY DIFFRACTIONf_plane_restr0.004361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5991-2.73610.31571440.27922334X-RAY DIFFRACTION100
2.7361-2.90750.30941310.25552395X-RAY DIFFRACTION100
2.9075-3.1320.29071230.22512375X-RAY DIFFRACTION100
3.132-3.44710.28641200.20252420X-RAY DIFFRACTION100
3.4471-3.94570.22751340.17622416X-RAY DIFFRACTION100
3.9457-4.97030.19071430.15552447X-RAY DIFFRACTION100
4.9703-48.04620.2311160.16852656X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.05244.1915-0.20546.4863-2.68522.87570.0873-0.5756-0.58770.894-0.36990.36580.7766-0.29640.32320.7753-0.10310.20310.4889-0.08130.41753.9582-0.204182.5901
27.21646.6575-2.5845.4012-2.3016-0.04850.1967-0.2038-0.13720.4222-0.2288-0.0799-0.1490.08310.02230.538-0.09910.0160.48030.07610.435934.18349.70681.9611
33.88862.745-3.84124.4116-3.62827.30180.5094-0.48190.14980.5416-0.421-0.2725-0.94060.4773-0.04030.4057-0.0265-0.05150.3037-0.05890.219871.730886.297350.4652
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1597 through 1627)
2X-RAY DIFFRACTION2(chain 'A' and (resid 1628 through 1725)) or (chain 'B' and (resid 1628 through 1725))
3X-RAY DIFFRACTION3chain 'B' and (resid 1595 through 1627)

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