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- PDB-6beh: Crystal structure of VACV D13 in complex with Rifapentine -

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Basic information

Entry
Database: PDB / ID: 6beh
TitleCrystal structure of VACV D13 in complex with Rifapentine
ComponentsScaffold protein D13
KeywordsVIRAL PROTEIN / poxvirus / scaffolding protein / Rifampicin resistance protein / immature virion
Function / homologyPoxvirus rifampicin-resistance / Poxvirus rifampicin resistance protein / response to antibiotic / identical protein binding / membrane / FORMIC ACID / RIFAPENTINE / Scaffold protein OPG125
Function and homology information
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 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 ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)187,72316
Polymers186,2303
Non-polymers1,49413
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, D13 protein elutes as a trimer (MW~180kDa)., microscopy, D13 trimers were confirmed by TEM.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19230 Å2
ΔGint-108 kcal/mol
Surface area62940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.790, 190.790, 253.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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: 62076.656 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus (strain Western Reserve)
Strain: Western Reserve / Gene: VACWR118, D13L / Plasmid: pPROEX-HTa / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P68440
#2: Chemical ChemComp-RPT / RIFAPENTINE / (2R,16S,17R,18R,19R,20S,21S,22S,23S)-8-{[(4-CYCLOPENTYLPIPERAZIN-1-YL)IMINO]METHYL}-5,6,9,17,19-PENTAHYDROXY-23-METHOXY -2,4,12,16,18,20,22-HEPTAMETHYL-1,11-DIOXO-1,2-DIHYDRO-2,7-(EPOXYPENTADECA[1,11,13]TRIENOIMINO)NAPHTHO[2,1-B]FURAN-21-YL ACETATE / 3-(((4-CYCLOPENTYL-1-PIPERAZINYL)IMINO)METHYL)RIFAMYCIN


Mass: 877.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H64N4O12
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE AUTHORS ACKNOWLEDGE THE PRESENCE OF UNMODELLED DENSITY AT THE LIGAND REGION, SUGGESTIVE OF A ...THE AUTHORS ACKNOWLEDGE THE PRESENCE OF UNMODELLED DENSITY AT THE LIGAND REGION, SUGGESTIVE OF A POSSIBLE SECOND/ALTERNATIVE CONFORMATION OF THE LIGAND. THIS DENSITY IS HOWEVER NOT STRONG ENOUGH TO BE MODELLED CONFIDENTLY

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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: 3.58 Å3/Da / Density % sol: 65.61 % / Description: hexagonal bypiramidal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: 3.5-4.0 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: 3→29.68 Å / Num. obs: 53571 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 15.741 % / Biso Wilson estimate: 73.22 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.215 / Rrim(I) all: 0.222 / Χ2: 0.92 / Net I/σ(I): 15.47
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3-3.0815.7031.3822.2639290.6081.4398.4
3.08-3.1615.8891.1122.7838070.7071.1598.6
3.16-3.2615.8720.8753.5737350.7970.90598.5
3.26-3.3615.9040.6554.7336240.8820.67898.5
3.36-3.4715.8970.4776.535120.9330.49498.4
3.47-3.5915.8650.3728.334030.9540.38598.2
3.59-3.7215.8710.3269.4632660.9670.33898.1
3.72-3.8815.8620.27411.1831610.9740.28398
3.88-4.0515.8720.20314.7630420.9880.2197.9
4.05-4.2515.8450.15818.5629110.9920.16497.8
4.25-4.4815.7630.13121.9827670.9940.13597.9
4.48-4.7515.8140.11424.7926240.9950.11897.5
4.75-5.0715.7680.1125.5524520.9960.11397.3
5.07-5.4815.7480.11923.7923110.9950.12497.1
5.48-615.6310.12322.9321330.9950.12797.2
6-6.7115.5940.11424.4119230.9960.11896.5
6.71-7.7515.4160.08929.8517230.9980.09296.5
7.75-9.4915.2480.05444.1114660.9990.05695.9
9.49-13.4314.8120.03560.41116110.03695.3
13.43-29.6813.4480.03659.0962110.03783.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XSCALEdata scaling
BUSTER2.1phasing
Cootmodel building
PDB_EXTRACTdata extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 3SAM

3sam


Resolution: 3→29.68 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.903 / SU R Cruickshank DPI: 2.011 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 3.459 / SU Rfree Blow DPI: 0.334 / SU Rfree Cruickshank DPI: 0.338
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2668 4.98 %RANDOM
Rwork0.198 ---
obs0.199 53571 97.5 %-
Displacement parametersBiso mean: 51.98 Å2
Baniso -1Baniso -2Baniso -3
1-3.168 Å20 Å20 Å2
2--3.168 Å20 Å2
3----6.3359 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: 1 / Resolution: 3→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12673 0 103 263 13039
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00813115HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9717855HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4411SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes329HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1952HARMONIC5
X-RAY DIFFRACTIONt_it13115HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.13
X-RAY DIFFRACTIONt_other_torsion17.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1833SEMIHARMONIC5
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_contact14856SEMIHARMONIC4
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3064 192 5.03 %
Rwork0.2673 3623 -
all0.2693 3815 -
obs--95.29 %

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