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- PDB-8f65: Crystal structure of VACV D13 in complex with BBL030900 -

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Basic information

Entry
Database: PDB / ID: 8f65
TitleCrystal structure of VACV D13 in complex with BBL030900
ComponentsScaffold protein D13
KeywordsVIRAL PROTEIN / poxvirus / assembly / scaffolding protein / Fragment-based drug design / immature virion
Function / homologyPoxvirus rifampicin-resistance / Poxvirus rifampicin resistance protein / response to antibiotic / identical protein binding / membrane / FORMIC ACID / 8-methoxyquinolin-4-amine / Scaffold protein OPG125
Function and homology information
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsSubedi, B.P. / Garriga, D. / Coulibaly, F.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1051907 Australia
Citation
Journal: To Be Published
Title: Structure of scaffolidng protein D13 of Vaccinia Virus in complex with fragments inhibiting A17 binding.
Authors: Subedi, B.P. / Garriga, D. / Coulibaly, F.
#1: Journal: Proc Natl Acad Sci U S A / Year: 2018
Title: Structural basis for the inhibition of poxvirus assembly by the antibiotic rifampicin.
Authors: Garriga, D. / Headey, S. / Accurso, C. / Gunzburg, M. / Scanlon, M. / Coulibaly, F.
History
DepositionNov 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Scaffold protein D13
B: Scaffold protein D13
C: Scaffold protein D13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,75335
Polymers195,1533
Non-polymers1,60132
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20460 Å2
ΔGint-116 kcal/mol
Surface area63700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.078, 191.078, 254.717
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Scaffold protein D13 / 62 kDa protein / Rifampicin resistance protein


Mass: 65050.840 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Gene: VACWR118, D13L
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P68440
#2: Chemical...
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-QF6 / 8-methoxyquinolin-4-amine


Mass: 174.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.44 Å3/Da / Density % sol: 64.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: 1.7 - 2.2 M sodium formate and 0.1 M citric acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.85→47.77 Å / Num. obs: 64478 / % possible obs: 100 % / Redundancy: 24.5 % / Biso Wilson estimate: 53.09 Å2 / CC1/2: 0.996 / Net I/σ(I): 25.2
Reflection shellResolution: 2.85→2.92 Å / Mean I/σ(I) obs: 3.7 / Num. unique obs: 4476 / CC1/2: 0.873

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Processing

Software
NameVersionClassification
PHENIX1.20rc4_4425refinement
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BEI

6bei


Resolution: 2.85→46.26 Å / SU ML: 0.3617 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.914
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2392 3255 5.06 %
Rwork0.1729 61093 -
obs0.1762 64348 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.58 Å2
Refinement stepCycle: LAST / Resolution: 2.85→46.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12700 0 106 410 13216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008213123
X-RAY DIFFRACTIONf_angle_d0.921217830
X-RAY DIFFRACTIONf_chiral_restr0.05662065
X-RAY DIFFRACTIONf_plane_restr0.00762281
X-RAY DIFFRACTIONf_dihedral_angle_d5.93781788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.890.38061280.27292623X-RAY DIFFRACTION100
2.89-2.940.30481550.25082585X-RAY DIFFRACTION100
2.94-2.990.30951540.23232616X-RAY DIFFRACTION99.96
2.99-3.040.36381350.23752606X-RAY DIFFRACTION100
3.04-3.090.31641500.20492620X-RAY DIFFRACTION99.96
3.09-3.150.31251310.20872603X-RAY DIFFRACTION99.96
3.15-3.220.28751390.21222636X-RAY DIFFRACTION100
3.22-3.290.27481180.20312640X-RAY DIFFRACTION100
3.29-3.360.28021380.20692617X-RAY DIFFRACTION99.96
3.36-3.450.30251620.19912614X-RAY DIFFRACTION99.96
3.45-3.540.26231410.18622638X-RAY DIFFRACTION99.82
3.54-3.640.26151520.16692603X-RAY DIFFRACTION99.96
3.64-3.760.22861510.16912624X-RAY DIFFRACTION99.96
3.76-3.90.21951390.15652664X-RAY DIFFRACTION99.96
3.9-4.050.19671320.14722644X-RAY DIFFRACTION99.71
4.05-4.240.18231180.13562657X-RAY DIFFRACTION99.78
4.24-4.460.19561360.1262676X-RAY DIFFRACTION99.93
4.46-4.740.17371260.12032682X-RAY DIFFRACTION99.86
4.74-5.10.16491490.12472676X-RAY DIFFRACTION100
5.1-5.620.19581550.14122689X-RAY DIFFRACTION99.96
5.62-6.430.20011420.16132714X-RAY DIFFRACTION100
6.43-8.090.24481450.19032764X-RAY DIFFRACTION100
8.09-46.260.28691590.21842902X-RAY DIFFRACTION99.19

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