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- PDB-4tt1: Crystal structure of fragment 1600-1733 of HSV1 UL36, native -

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Basic information

Entry
Database: PDB / ID: 4tt1
TitleCrystal structure of fragment 1600-1733 of HSV1 UL36, native
ComponentsDeneddylase
KeywordsHYDROLASE / Fibrous protein / Tegument Protein / VIRAL PROTEIN / PROTEIN FIBRIL
Function / homology
Function and homology information


nuclear capsid assembly / deNEDDylase activity / viral tegument / symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / deubiquitinase activity / viral DNA genome replication / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / host cell cytoplasm ...nuclear capsid assembly / deNEDDylase activity / viral tegument / symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / deubiquitinase activity / viral DNA genome replication / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / host cell cytoplasm / 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
PHOSPHATE ION / Large tegument protein deneddylase
Similarity search - Component
Biological speciesHerpes simplex virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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 1.3Dec 20, 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

Downloads & links

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Assembly

Deposited unit
A: Deneddylase
B: Deneddylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3764
Polymers30,1862
Non-polymers1902
Water1629
1
A: Deneddylase
B: Deneddylase
hetero molecules

A: Deneddylase
B: Deneddylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7528
Polymers60,3724
Non-polymers3804
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+2/31
Buried area11580 Å2
ΔGint-88 kcal/mol
Surface area31670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.217, 110.217, 159.939
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


Mass: 15093.057 Da / Num. of mol.: 2 / Fragment: Residues 1625-1757
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Herpes simplex virus (type 1 / strain 17)
Gene: UL36 / Production host: Escherichia coli (E. coli)
References: UniProt: P10220, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 4.65 Å3/Da / Density % sol: 73.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 200 mM diammonium hydrogenophosphate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97911 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.75→38.317 Å / Num. obs: 15531 / % possible obs: 99.9 % / Redundancy: 12.8 % / Net I/σ(I): 21
Reflection shellResolution: 2.6→2.75 Å / Redundancy: 12.4 % / Mean I/σ(I) obs: 1.82

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TT0

4tt0


Resolution: 2.75→38.317 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 769 4.96 %Random selection
Rwork0.2012 ---
obs0.2032 15518 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→38.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 0 10 9 1942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091948
X-RAY DIFFRACTIONf_angle_d1.142639
X-RAY DIFFRACTIONf_dihedral_angle_d13.368729
X-RAY DIFFRACTIONf_chiral_restr0.045316
X-RAY DIFFRACTIONf_plane_restr0.004350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7499-2.96210.4161540.34882863X-RAY DIFFRACTION100
2.9621-3.260.371500.30262881X-RAY DIFFRACTION100
3.26-3.73140.28431510.2352915X-RAY DIFFRACTION100
3.7314-4.69990.21151670.18452940X-RAY DIFFRACTION100
4.6999-38.32070.19391470.15863150X-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)
15.98551.52530.63622.2261-0.98135.9575-0.0761-0.4605-0.5220.19520.44671.63090.8958-0.2502-0.54140.87140.03690.15190.93820.01971.18995.52240.905185.64
29.16457.5317-2.97646.5635-2.26760.59780.2472-0.573-0.15490.3305-0.36180.0032-0.1520.20950.12340.6141-0.0531-0.00370.92590.2010.657133.990849.483784.1435
35.21874.4455-3.52459.4868-3.68634.55470.7298-0.9922-0.260.5321-0.581-0.8723-1.10161.0669-0.3220.6024-0.0955-0.04150.6229-0.05160.624671.292985.82551.9116
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1600 through 1627)
2X-RAY DIFFRACTION2(chain 'A' and (resid 1628 through 1723)) or (chain 'B' and (resid 1628 through 1723))
3X-RAY DIFFRACTION3chain 'B' and (resid 1595 through 1627)

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