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- PDB-8f47: Crystal structure of VACV D13 in complex with STK69439 -

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Basic information

Entry
Database: PDB / ID: 8f47
TitleCrystal structure of VACV D13 in complex with STK69439
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 / 6,8-dimethoxy-2-methylquinolin-4-amine / Scaffold protein OPG125
Function and homology information
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 10, 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)196,52129
Polymers195,1533
Non-polymers1,36926
Water4,972276
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)190.522, 190.522, 257.948
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 4 or (resid 5 and (name...
d_2ens_1(chain "B" and (resid 4 or (resid 5 and (name...
d_3ens_1(chain "C" and (resid 4 through 9 or resid 16...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1THRGLYA5 - 73
d_12ens_1PHEILEA75 - 183
d_13ens_1ASPGLUA185 - 308
d_14ens_1GLYASNA310 - 506
d_15ens_1PROMETA508 - 538
d_16ens_1FMTFMTC
d_17ens_1FMTFMTD
d_18ens_1FMTFMTE
d_19ens_1FMTFMTF
d_21ens_1THRLEUG5 - 10
d_22ens_1ILEASNG13 - 42
d_23ens_1ASNGLYG45 - 77
d_24ens_1PHEILEG79 - 187
d_25ens_1ASPGLUG189 - 312
d_26ens_1GLYASNG314 - 510
d_27ens_1PROMETG512 - 542
d_28ens_1FMTFMTH
d_29ens_1FMTFMTI
d_210ens_1FMTFMTJ
d_211ens_1FMTFMTK
d_31ens_1THRLEUL1 - 6
d_32ens_1ILEGLYL8 - 70
d_33ens_1PHEILEL72 - 180
d_34ens_1ASPGLUL182 - 305
d_35ens_1GLYASNL307 - 503
d_36ens_1PROMETL505 - 535
d_37ens_1FMTFMTO
d_38ens_1FMTFMTP
d_39ens_1FMTFMTQ
d_310ens_1FMTFMTR

NCS oper:
IDCodeMatrixVector
1given(-0.245511858376, -0.747643372423, -0.617052116979), (0.832974114858, -0.488301767857, 0.260222034969), (-0.495860919384, -0.450100845566, 0.742651450849)219.449722054, 65.7890516665, 103.509110556
2given(-0.255921329971, 0.826910115661, -0.50072341016), (-0.7355516593, -0.502672138672, -0.454185510011), (-0.627270300083, 0.252072175418, 0.736879629935)52.5661482557, 242.747776064, 43.6128582487

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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.: 25 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-XDF / 6,8-dimethoxy-2-methylquinolin-4-amine


Mass: 218.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 3.46 Å3/Da / Density % sol: 64.48 %
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: 3.1→47.63 Å / Num. obs: 50722 / % possible obs: 100 % / Redundancy: 22 % / Biso Wilson estimate: 56.8 Å2 / CC1/2: 0.993 / Net I/σ(I): 13.1
Reflection shellResolution: 3.1→3.2 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4589 / CC1/2: 0.733 / % possible all: 100

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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: 3.1→26.04 Å / SU ML: 0.3983 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.9508
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2319 2537 5.02 %
Rwork0.1677 48008 -
obs0.1709 50545 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.37 Å2
Refinement stepCycle: LAST / Resolution: 3.1→26.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12687 0 91 276 13054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010413101
X-RAY DIFFRACTIONf_angle_d1.134217808
X-RAY DIFFRACTIONf_chiral_restr0.06792068
X-RAY DIFFRACTIONf_plane_restr0.00922279
X-RAY DIFFRACTIONf_dihedral_angle_d5.12921783
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.77277435148
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.639354499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.160.35041430.26642615X-RAY DIFFRACTION100
3.16-3.220.32851280.24822636X-RAY DIFFRACTION100
3.22-3.290.31251220.23452651X-RAY DIFFRACTION100
3.29-3.370.2991370.21082625X-RAY DIFFRACTION100
3.37-3.450.26781560.19452594X-RAY DIFFRACTION100
3.45-3.550.26241440.17742628X-RAY DIFFRACTION99.96
3.55-3.650.22261580.17332612X-RAY DIFFRACTION100
3.65-3.770.26231520.16362617X-RAY DIFFRACTION100
3.77-3.90.21751320.15572655X-RAY DIFFRACTION100
3.9-4.060.2181370.14452645X-RAY DIFFRACTION100
4.06-4.240.22031160.13612669X-RAY DIFFRACTION100
4.24-4.470.1681330.11982675X-RAY DIFFRACTION100
4.47-4.740.18231320.12032668X-RAY DIFFRACTION100
4.74-5.110.1681420.12232678X-RAY DIFFRACTION100
5.11-5.620.21381620.13972683X-RAY DIFFRACTION100
5.62-6.420.18161420.15962713X-RAY DIFFRACTION100
6.42-8.050.241430.18762757X-RAY DIFFRACTION100
8.05-26.040.27271580.21822887X-RAY DIFFRACTION99.64

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