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- PDB-6bef: Crystal structure of VACV D13 in complex with 3-formyl rifamycin SV -

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Basic information

Entry
Database: PDB / ID: 6bef
TitleCrystal structure of VACV D13 in complex with 3-formyl rifamycin SV
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 / Chem-3YI / FORMIC ACID / Scaffold protein OPG125
Function and homology information
Biological speciesVaccinia virus WR
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.21 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

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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)187,69618
Polymers186,2303
Non-polymers1,46615
Water4,612256
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 area18540 Å2
ΔGint-89 kcal/mol
Surface area63360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.060, 191.060, 254.320
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: 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-3YI / (2S,12Z,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-8-formyl-5,6,9,17,19-pentahydroxy-23-methoxy-2,4,12,16,18,20,22-heptam ethyl-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienoimino)naphtho[2,1-b]furan-21-yl acetate / 3-formyl rifamycin SV


Mass: 725.779 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H47NO13
#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.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 3.6 Å3/Da / Density % sol: 65.81 % / 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 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: 3.21→19.96 Å / Num. obs: 45431 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 15.325 % / Biso Wilson estimate: 74.72 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.326 / Rrim(I) all: 0.337 / Χ2: 0.881 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.21-3.2915.4121.7181.9432870.6311.77799.8
3.29-3.3815.6171.2832.5532070.7741.326100
3.38-3.4815.6160.9963.3431520.8541.03100
3.48-3.5915.5930.7934.1830380.8960.82100
3.59-3.715.5730.6784.8829410.9210.70199.9
3.7-3.8315.5670.5745.6528790.940.593100
3.83-3.9815.5540.4457.3327710.9690.46100
3.98-4.1415.5120.349.4326590.980.351100
4.14-4.3215.4970.27911.2525600.9860.288100
4.32-4.5415.4350.22613.624740.9910.234100
4.54-4.7815.3940.2114.6523410.9920.217100
4.78-5.0715.3540.19315.3922100.9930.2100
5.07-5.4215.260.21114.2821060.9940.218100
5.42-5.8615.2580.22813.3319480.990.236100
5.86-6.4115.0560.1915.4818310.9920.196100
6.41-7.1715.0070.18315.8816590.9950.19100
7.17-8.2814.80.12421.8314830.9980.128100
8.28-10.1414.4780.07232.912730.9990.074100
10.14-14.3413.9770.05339.7410160.9990.055100
14.34-19.9612.1070.05634.835960.9990.05896.4

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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: 3.21→19.96 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.891 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.377
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2255 5 %RANDOM
Rwork0.195 ---
obs0.197 45091 100 %-
Displacement parametersBiso max: 147.8 Å2 / Biso mean: 58.35 Å2 / Biso min: 7.68 Å2
Baniso -1Baniso -2Baniso -3
1-4.2689 Å20 Å20 Å2
2--4.2689 Å20 Å2
3----8.5377 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: final / Resolution: 3.21→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12624 0 100 256 12980
Biso mean--90.63 36.65 -
Num. residues----1612
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4401SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes325HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1949HARMONIC5
X-RAY DIFFRACTIONt_it13091HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1835SEMIHARMONIC5
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_contact14612SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d13091HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg17826HARMONIC20.92
X-RAY DIFFRACTIONt_omega_torsion2
X-RAY DIFFRACTIONt_other_torsion18.19
LS refinement shellResolution: 3.21→3.29 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2559 158 4.81 %
Rwork0.2492 3129 -
all0.2496 3287 -
obs--99.94 %

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