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- PDB-8qln: Crystal structure of an N-terminal fragment of HCMV UL47 -

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Basic information

Entry
Database: PDB / ID: 8qln
TitleCrystal structure of an N-terminal fragment of HCMV UL47
ComponentsInner tegument protein
KeywordsVIRAL PROTEIN / HCMV / tegument protein
Function / homologyHerpesvirus tegument protein U30 / Herpes virus tegument protein U30 / Inner tegument protein / viral tegument / virion assembly / host cell Golgi apparatus / host cell nucleus / 6-tungstotellurate(VI) / Inner tegument protein
Function and homology information
Biological speciesHuman herpesvirus 5 strain AD169
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.51 Å
AuthorsRehfeld, C.L. / Reubold, T.F. / Eschenburg, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2155 RESIST Project ID 390874280 Germany
CitationJournal: To be published
Title: Crystal structure of an N-terminal fragment of HCMV UL47
Authors: Rehfeld, C.L. / Reubold, T.F. / Eschenburg, S.
History
DepositionSep 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inner tegument protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8022
Polymers62,1881
Non-polymers1,6151
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.960, 64.960, 265.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Inner tegument protein


Mass: 62187.801 Da / Num. of mol.: 1 / Mutation: E161S, R162S, R163G, K165S, K166S, Q280S, K281S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 5 strain AD169 / Strain: AD169 / Gene: UL47 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P16784
#2: Chemical ChemComp-TEW / 6-tungstotellurate(VI)


Mass: 1614.626 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O24TeW6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.39 Å3/Da / Density % sol: 48.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M Sodium acetate pH 4.6, 2 M sodium formate, 5 mM TEW

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2.51→46.46 Å / Num. obs: 20390 / % possible obs: 100 % / Redundancy: 25.3 % / Biso Wilson estimate: 68.61 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.109 / Net I/σ(I): 18.35
Reflection shellResolution: 2.51→2.6 Å / Redundancy: 27 % / Num. unique obs: 1930 / CC1/2: 0.918 / Rrim(I) all: 1.043 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.51→46.44 Å / SU ML: 0.3231 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.7595
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2511 1019 5 %
Rwork0.2145 19367 -
obs0.2164 19367 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.21 Å2
Refinement stepCycle: LAST / Resolution: 2.51→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3806 0 31 33 3870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00163932
X-RAY DIFFRACTIONf_angle_d0.38015403
X-RAY DIFFRACTIONf_chiral_restr0.0345595
X-RAY DIFFRACTIONf_plane_restr0.0028677
X-RAY DIFFRACTIONf_dihedral_angle_d11.72091421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.650.28581410.25062671X-RAY DIFFRACTION100
2.65-2.810.29611430.22742718X-RAY DIFFRACTION100
2.81-3.030.29881420.25232704X-RAY DIFFRACTION100
3.03-3.330.31571430.27722721X-RAY DIFFRACTION99.97
3.33-3.820.26681470.24552779X-RAY DIFFRACTION100
3.82-4.810.24471460.19692776X-RAY DIFFRACTION100
4.81-46.440.21781570.18922998X-RAY DIFFRACTION99.84

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