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- PDB-6bee: Crystal structure of VACV D13 in complex with Rifaximin -

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Basic information

Entry
Database: PDB / ID: 6bee
TitleCrystal structure of VACV D13 in complex with Rifaximin
ComponentsScaffold protein D13Scaffolding
KeywordsVIRAL PROTEIN / poxvirus / assembly / scaffolding protein / Rifampicin resistance protein / immature virion
Function / homologyPoxvirus rifampicin-resistance / Poxvirus rifampicin resistance protein / response to antibiotic / membrane / identical protein binding / FORMIC ACID / Chem-RXM / Scaffold protein OPG125
Function and homology information
Biological speciesVaccinia virus WR
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.11 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 / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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)187,49413
Polymers186,2303
Non-polymers1,26410
Water5,008278
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 area18000 Å2
ΔGint-97 kcal/mol
Surface area63350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.140, 191.140, 253.270
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 / Scaffolding / 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 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 / Formic acid


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-RXM / (2S,16Z,18E,20S,21S,22R,23R,24R,25S,26R,27S,28E)-5,6,21,23-tetrahydroxy-27-methoxy-2,4,11,16,20,22,24,26-octamethyl-1,1 5-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienoimino)furo[2'',3'':7',8']naphtho[1',2':4,5]imidazo[1,2-a]pyridin-2 5-yl acetate / Rifaximin / Rifaximin


Mass: 785.879 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H51N3O11 / Comment: antibiotic*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 3.59 Å3/Da / Density % sol: 65.7 % / Description: hexagonal bypiramidal
Crystal growTemperature: 298 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 210 / 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: 3.11→20 Å / Num. obs: 49697 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 22.118 % / Biso Wilson estimate: 75.44 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.33 / Rrim(I) all: 0.337 / Χ2: 0.902 / Net I/σ(I): 12.96
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.11-3.1922.082.0441.8935790.6472.09298.6
3.19-3.2722.6031.5122.5835110.7861.547100
3.27-3.3722.5271.183.3334280.8421.207100
3.37-3.4722.5050.8724.4933430.9160.892100
3.47-3.5922.4780.6915.6632170.9410.707100
3.59-3.7122.4470.5926.6131330.9580.606100
3.71-3.8522.390.5057.6930480.9680.516100
3.85-4.0122.4010.37810.1829230.9840.387100
4.01-4.1922.3540.29912.7228000.9880.306100
4.19-4.3922.2710.24715.126910.9920.253100
4.39-4.6322.2380.19918.425650.9950.204100
4.63-4.9122.1590.18619.5924380.9950.19100
4.91-5.2522.0820.1919.0422930.9950.194100
5.25-5.6721.9440.2117.3821580.9950.215100
5.67-6.2121.8370.18818.9319940.9950.192100
6.21-6.9521.630.1819.5918060.9960.185100
6.95-8.0221.3810.12626.0316200.9980.129100
8.02-9.8220.9920.07339.38138510.074100
9.82-13.8920.2420.04852.08111810.049100
13.89-2017.770.05245.4664710.05396.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTERrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Cootmodel building
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 3SAM

3sam


Resolution: 3.11→20 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.897 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.345
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2455 4.98 %RANDOM
Rwork0.197 ---
obs0.198 49339 100 %-
Displacement parametersBiso max: 127.54 Å2 / Biso mean: 56.32 Å2 / Biso min: 10.64 Å2
Baniso -1Baniso -2Baniso -3
1-4.3445 Å20 Å20 Å2
2--4.3445 Å20 Å2
3----8.6889 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: final / Resolution: 3.11→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12668 0 88 278 13034
Biso mean--89.37 38.47 -
Num. residues----1613
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4409SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes333HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1900HARMONIC5
X-RAY DIFFRACTIONt_it13095HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1831SEMIHARMONIC5
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_contact14792SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d13095HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg17833HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion2.11
X-RAY DIFFRACTIONt_other_torsion17.18
LS refinement shellResolution: 3.11→3.19 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3186 161 4.49 %
Rwork0.2618 3427 -
all0.2644 3588 -
obs--99.97 %

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