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- PDB-8ua2: Crystal Structure of infected cell protein 0 (ICP0) from herpes s... -

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Basic information

Entry
Database: PDB / ID: 8ua2
TitleCrystal Structure of infected cell protein 0 (ICP0) from herpes simplex virus 1 (proteolyzed fragment)
ComponentsRL2
KeywordsPROTEIN BINDING / infected cell protein 0 (ICP0) / herpes simplex virus 1 / beta barrel / dimization
Function / homology
Function and homology information


ligase activity / ubiquitin protein ligase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / protein ubiquitination / metal ion binding
Similarity search - Function
Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Biological speciesHuman alphaherpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsLovell, S. / Kashipathy, M. / Battaile, K.P. / Cooper, A. / Davido, D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM1110761 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM113117 United States
CitationJournal: Proteins / Year: 2024
Title: HSV-1 ICP0 dimer domain adopts a novel beta-barrel fold.
Authors: McCloskey, E. / Kashipathy, M. / Cooper, A. / Gao, P. / Johnson, D.K. / Battaile, K.P. / Lovell, S. / Davido, D.J.
History
DepositionSep 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RL2
B: RL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7974
Polymers77,5442
Non-polymers2542
Water00
1
A: RL2
B: RL2
hetero molecules

A: RL2
B: RL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,5958
Polymers155,0874
Non-polymers5084
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area15640 Å2
ΔGint-113 kcal/mol
Surface area17230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.909, 95.909, 74.526
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein RL2 / Ubiquitin E3 ligase ICP0


Mass: 38771.777 Da / Num. of mol.: 2 / Fragment: A391-Q776
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 1 (Herpes simplex virus type 1)
Gene: RL2, RL2_1, HHV1gp002, HHV1gp082 / Plasmid: pTBSG / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: H9E965
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PACT G3: 20% (w/v) PEG 3350, 100 mM Bis-Tris Propane pH 7.5, 200 mM NaI, 80% crystallization solution and 20% (v/v) PEG 200. The electron density was consistent with a protelyzed fragment spanning A636-Q776

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2018
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→47.95 Å / Num. obs: 10603 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.036 / Rrim(I) all: 0.128 / Χ2: 0.99 / Net I/σ(I): 14.6 / Num. measured all: 134156
Reflection shellResolution: 2.65→2.78 Å / % possible obs: 99.9 % / Redundancy: 13.4 % / Rmerge(I) obs: 1.452 / Num. measured all: 18440 / Num. unique obs: 1373 / CC1/2: 0.862 / Rpim(I) all: 0.41 / Rrim(I) all: 1.509 / Χ2: 0.94 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX(dev_3083: ???)refinement
Aimlessdata scaling
XDSdata reduction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.65→34.734 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 31.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2882 511 4.85 %
Rwork0.2182 --
obs0.2213 10544 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→34.734 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1684 0 2 0 1686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091725
X-RAY DIFFRACTIONf_angle_d1.1362369
X-RAY DIFFRACTIONf_dihedral_angle_d11.6651011
X-RAY DIFFRACTIONf_chiral_restr0.063288
X-RAY DIFFRACTIONf_plane_restr0.011296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6502-2.91680.37881310.2932436X-RAY DIFFRACTION100
2.9168-3.33860.31751260.2562458X-RAY DIFFRACTION100
3.3386-4.20510.30231400.20812491X-RAY DIFFRACTION100
4.2051-34.7340.24941140.20232648X-RAY DIFFRACTION100

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