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- PDB-6bei: Crystal structure of VACV D13 in its apo (unbound) form -

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Basic information

Entry
Database: PDB / ID: 6bei
TitleCrystal structure of VACV D13 in its apo (unbound) form
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 / Scaffold protein OPG125
Function and homology information
Biological speciesVaccinia virus WR
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 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)186,89216
Polymers186,2303
Non-polymers66213
Water6,521362
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 area17860 Å2
ΔGint-99 kcal/mol
Surface area63910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.820, 190.820, 254.240
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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 362 / 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: 65.71 % / 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: 2.81→19.94 Å / Num. obs: 66970 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 15.432 % / Biso Wilson estimate: 71.99 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.2 / Rrim(I) all: 0.207 / Χ2: 0.935 / Net I/σ(I): 17.17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.81-2.8815.3711.7881.7947920.5611.8598.4
2.88-2.9615.6831.3682.3647730.7131.414100
2.96-3.0415.6881.0792.9946120.7991.115100
3.04-3.1415.6540.8273.8945240.8670.855100
3.14-3.2415.6580.654.9443810.9180.672100
3.24-3.3515.6350.4766.7242190.9540.492100
3.35-3.4815.6270.3349.5141080.9780.345100
3.48-3.6215.5840.25912.2139200.9840.268100
3.62-3.7815.5920.2241437930.9890.232100
3.78-3.9715.5520.17417.6136440.9940.18100
3.97-4.1815.480.1323.0334640.9960.135100
4.18-4.4415.5080.10428.1332840.9970.107100
4.44-4.7415.3710.08832.2531030.9980.09199.9
4.74-5.1215.3550.08333.4228890.9980.086100
5.12-5.6115.2790.09130.8826880.9980.095100
5.61-6.2715.1390.08931.2124330.9980.092100
6.27-7.2514.9550.08332.9221790.9990.086100
7.25-8.8714.7250.05346.7218670.9990.055100
8.87-12.5514.2870.0368.42148410.031100
12.55-19.9412.7680.02968.9881310.0390.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Cootmodel building
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 3SAM

3sam


Resolution: 2.81→19.94 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.901 / SU R Cruickshank DPI: 0.538 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.55 / SU Rfree Blow DPI: 0.285 / SU Rfree Cruickshank DPI: 0.288
RfactorNum. reflection% reflectionSelection details
Rfree0.231 3378 5.07 %RANDOM
Rwork0.198 ---
obs0.2 66602 100 %-
Displacement parametersBiso max: 124.99 Å2 / Biso mean: 51.23 Å2 / Biso min: 21.04 Å2
Baniso -1Baniso -2Baniso -3
1-3.2841 Å20 Å20 Å2
2--3.2841 Å20 Å2
3----6.5682 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: final / Resolution: 2.81→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12690 0 43 362 13095
Biso mean--59.99 44.49 -
Num. residues----1613
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4413SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes320HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1870HARMONIC5
X-RAY DIFFRACTIONt_it13046HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1821SEMIHARMONIC5
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_contact14774SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d13046HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg17745HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion2.3
X-RAY DIFFRACTIONt_other_torsion17.17
LS refinement shellResolution: 2.81→2.88 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3068 244 5.05 %
Rwork0.2733 4588 -
all0.275 4832 -
obs--99.94 %

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