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- PDB-8bq1: Herpes simplex virus type 1 protease -

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Basic information

Entry
Database: PDB / ID: 8bq1
TitleHerpes simplex virus type 1 protease
ComponentsAssemblin
KeywordsVIRAL PROTEIN / herpes / protease / UL26 / VP24
Function / homology
Function and homology information


assemblin / nuclear capsid assembly / viral release from host cell / host cell cytoplasm / serine-type endopeptidase activity / host cell nucleus / proteolysis / identical protein binding
Similarity search - Function
Peptidase S21 / Herpesvirus protease superfamily / Assemblin (Peptidase family S21)
Similarity search - Domain/homology
Capsid scaffolding protein
Similarity search - Component
Biological speciesHuman alphaherpesvirus 1 strain 17
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsPachota, M. / Grzywa, R. / Plewka, J. / Wilk, P. / Mackereth, C. / Czarna, A. / Sienczyk, M. / Pyrc, K.
Funding support Poland, 2items
OrganizationGrant numberCountry
Polish National Science Centre2017/27/N/NZ6/02328 Poland
Foundation for Polish ScienceTEAM TECH CORE FACILITY/2017-4/6 Poland
CitationJournal: To Be Published
Title: Herpes simplex virus type 1 protease
Authors: Pachota, M.
History
DepositionNov 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Assemblin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7442
Polymers26,6511
Non-polymers921
Water18010
1
A: Assemblin
hetero molecules

A: Assemblin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4874
Polymers53,3032
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Buried area3280 Å2
ΔGint-12 kcal/mol
Surface area18520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.080, 70.080, 77.330
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

21A-409-

HOH

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Components

#1: Protein Assemblin / Protease


Mass: 26651.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 1 strain 17 / Gene: UL26 / Production host: Escherichia coli (E. coli) / References: UniProt: P10210, assemblin
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.06 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 5% PEG400, 1.9M ammonium sulfate, 0.2M sodium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03323 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 1, 2022
RadiationMonochromator: LN2 cooled double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03323 Å / Relative weight: 1
ReflectionResolution: 2.32→47.74 Å / Num. obs: 9338 / % possible obs: 99.4 % / Redundancy: 20.47 % / Biso Wilson estimate: 64.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.13 / Rrim(I) all: 0.133 / Net I/σ(I): 15.93
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.32-2.4618.922.9181.2714590.55892.998997.6
2.46-2.631.82814090.7851.87399.9
2.63-2.841.12813330.9531.156
2.84-3.110.56812080.9810.583
3.11-3.470.27211170.9970.278
3.47-4.010.1299750.9980.132
4.01-4.90.0768190.9990.078
4.9-6.890.076550.9980.072
6.89-47.740.0673630.9980.069

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASER2.8.3phasing
PHENIX1.20.1_4487refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AT3

1at3


Resolution: 2.32→47.74 Å / SU ML: 0.4136 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.6949
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.244 466 5 %
Rwork0.1948 8849 -
obs0.1973 9315 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.14 Å2
Refinement stepCycle: LAST / Resolution: 2.32→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1475 0 6 10 1491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00251525
X-RAY DIFFRACTIONf_angle_d0.55862083
X-RAY DIFFRACTIONf_chiral_restr0.0403246
X-RAY DIFFRACTIONf_plane_restr0.0057273
X-RAY DIFFRACTIONf_dihedral_angle_d5.3194222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.660.32991530.29962892X-RAY DIFFRACTION98.16
2.66-3.350.28711550.25092970X-RAY DIFFRACTION99.68
3.35-47.740.22071580.1662987X-RAY DIFFRACTION99.56
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)
10.526850340963-0.2039466993390.01038829794641.16377690414-0.0945583742680.4637506840870.394326445288-0.254416007757-1.077999475680.7948583829320.354425041892-2.017240271270.4143684460591.120273861730.08716481007890.827683038744-0.108528021819-0.2026120534850.732716918321-0.008188468734580.79980629546844.902981278421.428776130444.0862311274
20.785404893894-0.09634645250760.3839863145851.16532069818-0.7241867288560.866481961543-0.0461311886575-0.0100206498613-0.0602525909777-0.2436923985250.03252694758390.433729102928-0.272031587719-0.1576692770920.0002691067195740.4991032715560.033679152166-0.03120772572630.478982998638-0.04033547728340.64023293964519.849105139311.821010405836.4713276329
30.561393746081-0.0234465330925-0.1604307601080.0212441819446-0.09738553842910.450024860860.00476654007975-0.1321968920320.3659778349470.2442318724530.16831870611-0.7608979937270.111606850092-0.2835841937750.0004468919403080.6481010782920.0111540585186-0.008195825331380.630312321924-0.02926844370630.63740098819146.13528434037.7935202186445.7068429872
40.9517892289780.0844174137065-0.3348574981811.290251554340.6850240558451.5798572109-0.00940655084889-0.126067940853-0.03540353833670.05161233050810.03265580081790.05768162586260.1345883344410.0117500554960.0008920686493120.5177310360570.01138216853550.06334463282310.5666369267790.03299339793190.59106524370326.60779911279.0454079279842.6668954613
50.221988669685-0.278285025109-0.03924310849590.3737312161150.1365788735950.1199636807390.1925803633650.417990627931-0.617393366204-1.1053182043-0.07647004085560.3522208852080.59085838790.2244484307810.002303114314050.736961046613-0.0534024065356-0.0707320028040.612416016064-0.02727921009710.6558091810730.19484854297.3336738423728.2207863574
60.8167817173811.25621328203-0.07754488906321.60193033619-0.2358525851790.2381978242130.006154510971480.299522936792-0.0934387868617-0.01759992334690.3567435365720.2353749950840.0516189857730.6571337627220.002262659325930.8111419261310.08068484926420.0003479775775990.651953660602-0.06963091332740.63334708167429.19527297418.408697172637.0338266393
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 11 through 20 )11 - 201 - 10
22chain 'A' and (resid 21 through 88 )21 - 8811 - 73
33chain 'A' and (resid 89 through 112 )89 - 11274 - 97
44chain 'A' and (resid 113 through 161 )113 - 16198 - 141
55chain 'A' and (resid 162 through 179 )162 - 179142 - 159
66chain 'A' and (resid 180 through 214 )180 - 214160 - 194

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