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- PDB-6bec: Crystal structure of VACV D13 in complex with Rifabutin -

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Basic information

Entry
Database: PDB / ID: 6bec
TitleCrystal structure of VACV D13 in complex with Rifabutin
ComponentsScaffold protein D13
KeywordsVIRAL PROTEIN / poxvirus / assembly / scaffolding protein / Rifampicin resistance protein / immature virion
Function / homologyPoxvirus rifampicin-resistance / Poxvirus rifampicin resistance protein / response to antibiotic / identical protein binding / membrane / FORMIC ACID / RIFABUTIN / Scaffold protein OPG125
Function and homology information
Biological speciesVaccinia virus WR
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.91 Å
AuthorsGarriga, D. / Accurso, C. / Coulibaly, F.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1051907 Australia
CitationJournal: 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
DepositionOct 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 15, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)196,71017
Polymers195,1533
Non-polymers1,55814
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, D13 protein elutes as a trimer (MW~180kDa)., microscopy, Trimers can be imaged by TEM.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19720 Å2
ΔGint-112 kcal/mol
Surface area65630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.620, 188.620, 261.550
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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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 WR / Strain: Western Reserve / Gene: VACWR118, D13L / Plasmid: pPROEX-HTa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P68440
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-RBT / RIFABUTIN / (9S,12E,14S,15R,16S,17R,18R,19R,20S,21S,22E,24Z)-6-16,18,20- TETRAHYDROXY-1'-ISOBUTYL-14-METHOXY-7,9,15,17,19,21,25- HEPTAMETHYLSPIRO(9,4-(EPOXYPENTADECA(1,11,13)TRIENIMINO)-2H- FURO(2',3':7,8)NAPHTH(1,2-D)IMIDAZOLE-2,4'-PIPERIDINE)- 5,10,26(3H,9H)-TRIONE,16-ACETATE / ANSAMYCIN


Mass: 847.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H62N4O11 / Comment: antibiotic, antiretroviral*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O

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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: 64.26 %
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
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 2, 2013
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.91→19.99 Å / Num. obs: 60691 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 15.369 % / Biso Wilson estimate: 68.5 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.271 / Rrim(I) all: 0.28 / Χ2: 0.92 / Net I/σ(I): 12.45
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.91-2.9815.0581.7331.8742960.6251.79397.5
2.98-3.0615.671.4432.2843130.7391.491100
3.06-3.1515.6491.1632.8341920.8011.202100
3.15-3.2515.6520.8973.6540890.8650.927100
3.25-3.3615.6420.6844.7839620.9190.707100
3.36-3.4715.60.5046.5238280.9570.521100
3.47-3.6115.6090.4028.1536960.9710.416100
3.61-3.7515.5740.3459.3135880.9790.356100
3.75-3.9215.5280.28411.0934320.9870.293100
3.92-4.1115.4950.21614.2632890.9920.223100
4.11-4.3315.4950.17417.3631320.9940.18100
4.33-4.615.4090.14220.6329910.9950.147100
4.6-4.9115.3780.13122.0627890.9960.136100
4.91-5.3115.2710.13221.3826340.9960.136100
5.31-5.8115.2140.14519.624270.9960.15100
5.81-6.515.0940.13320.8922230.9960.138100
6.5-7.5114.9080.11822.8819790.9970.122100
7.51-9.1914.6730.07731.4916870.9990.079100
9.19-1314.1620.04843.2813490.9990.05100
13-19.9912.3480.04542.357950.9990.04797.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTERrefinement
XSCALEdata scaling
Coot3.22model building
BUSTERrefinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 3SAM

3sam


Resolution: 2.91→19.99 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.897 / SU R Cruickshank DPI: 0.744 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.771 / SU Rfree Blow DPI: 0.303 / SU Rfree Cruickshank DPI: 0.307
RfactorNum. reflection% reflectionSelection details
Rfree0.226 3000 4.97 %RANDOM
Rwork0.195 ---
obs0.197 60407 100 %-
Displacement parametersBiso max: 149.8 Å2 / Biso mean: 49.81 Å2 / Biso min: 17.87 Å2
Baniso -1Baniso -2Baniso -3
1-3.0529 Å20 Å20 Å2
2--3.0529 Å20 Å2
3----6.1059 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: final / Resolution: 2.91→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12726 0 107 304 13137
Biso mean--70.39 39.53 -
Num. residues----1622
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4451SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes319HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1906HARMONIC5
X-RAY DIFFRACTIONt_it13160HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1841SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14678SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d13160HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg17920HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion2.23
X-RAY DIFFRACTIONt_other_torsion17.02
LS refinement shellResolution: 2.91→2.99 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2714 213 4.84 %
Rwork0.2682 4191 -
all0.2683 4404 -
obs--99.84 %

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