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- PDB-7tdq: Crystal structure of KSHV KicGAS/ORF52 -

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Basic information

Entry
Database: PDB / ID: 7tdq
TitleCrystal structure of KSHV KicGAS/ORF52
ComponentsTegument protein ORF52
KeywordsVIRAL PROTEIN / tegument protein / oligomerization / DNA-binding
Function / homologyHerpesvirus BLRF2 / Herpesvirus BLRF2 protein / viral tegument / : / double-stranded DNA binding / host cell cytoplasm / Tegument protein ORF52
Function and homology information
Biological speciesHuman herpesvirus 8 strain GK18
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYin, Q. / Tian, Y. / Bhowmik, D. / Zhu, F.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)R01DE026101 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI146330 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R00AI108793 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Structural basis of higher order oligomerization of KSHV inhibitor of cGAS.
Authors: Bhowmik, D. / Tian, Y. / Wang, B. / Zhu, F. / Yin, Q.
History
DepositionJan 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tegument protein ORF52
B: Tegument protein ORF52


Theoretical massNumber of molelcules
Total (without water)19,2472
Polymers19,2472
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-17 kcal/mol
Surface area12520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.332, 58.683, 138.421
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-125-

HOH

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Components

#1: Protein Tegument protein ORF52


Mass: 9623.736 Da / Num. of mol.: 2 / Mutation: L62M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 strain GK18 / Strain: isolate GK18 / Gene: ORF52 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): E. coli / References: UniProt: Q2HR80
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.81 Å3/Da / Density % sol: 56.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1 microL of protein (10 mg/ml) + 1 microL of reservoir solution of 9% (v/v) PEG3350, 100mM Na-citrate pH 4.5 + 0.2microL of the detergent additive n-Octyl-N,N-dimethyl-3-ammonio-1-propanesulfonate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 15886 / % possible obs: 98.3 % / Redundancy: 4.9 % / Biso Wilson estimate: 52.29 Å2 / CC1/2: 0.991 / CC star: 0.008 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.062 / Rrim(I) all: 0.142 / Rsym value: 0.102 / Χ2: 1.911 / Net I/σ(I): 19.78
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 1.32 / Num. unique obs: 1481 / CC1/2: 0.751 / CC star: 0.926 / Rpim(I) all: 0.351 / Rrim(I) all: 0.696 / Rsym value: 0.497 / Χ2: 0.661 / % possible all: 90.4

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OA5

2oa5


Resolution: 2.5→49.77 Å / SU ML: 0.3788 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 31.4291
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.265 1442 10.03 %
Rwork0.2246 12942 -
obs0.2286 14384 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.27 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 0 0 46 1328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00231286
X-RAY DIFFRACTIONf_angle_d0.50471732
X-RAY DIFFRACTIONf_chiral_restr0.032220
X-RAY DIFFRACTIONf_plane_restr0.0029222
X-RAY DIFFRACTIONf_dihedral_angle_d17.6757500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.590.38351350.3131243X-RAY DIFFRACTION94.77
2.59-2.690.35871440.32311282X-RAY DIFFRACTION98.21
2.69-2.820.34061480.29371300X-RAY DIFFRACTION99.45
2.82-2.960.34091490.29361318X-RAY DIFFRACTION99.93
2.96-3.150.31811410.27481291X-RAY DIFFRACTION99.79
3.15-3.390.3061490.26971292X-RAY DIFFRACTION99.93
3.39-3.730.28691430.22371306X-RAY DIFFRACTION99.66
3.73-4.270.25841450.18851295X-RAY DIFFRACTION99.24
4.27-5.380.18681420.18931314X-RAY DIFFRACTION100
5.38-49.770.22211460.18961301X-RAY DIFFRACTION98.64
Refinement TLS params.Method: refined / Origin x: 11.6371299098 Å / Origin y: 45.0483533591 Å / Origin z: 56.2487140621 Å
111213212223313233
T0.449907254487 Å2-0.0238863096334 Å20.0167245494127 Å2-0.371117777174 Å2-0.00349302480765 Å2--0.447481061929 Å2
L0.109863952348 °2-0.137501799373 °2-0.696783408523 °2--0.248095047856 °20.219281022652 °2--3.17530786762 °2
S-0.0607502235635 Å °-0.0677022573292 Å °-0.107695319118 Å °-0.0867478132299 Å °-0.06106751724 Å °-0.0332457004258 Å °0.0748686155512 Å °0.0757988226529 Å °0.155924742373 Å °
Refinement TLS groupSelection details: all

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