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- PDB-6cj6: Structure of the poxvirus protein F9 -

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Basic information

Entry
Database: PDB / ID: 6cj6
TitleStructure of the poxvirus protein F9
ComponentsProtein F9
KeywordsVIRAL PROTEIN / entry fusion complex associated protein
Function / homology
Function and homology information


viral envelope / virion membrane / membrane
Similarity search - Function
Virion membrane protein, poxvirus L1-related / Lipid membrane protein of large eukaryotic DNA viruses
Similarity search - Domain/homology
ETHANOL / Chem-ETE / 2-ETHOXYETHANOL / METHANOL / 1,3-PROPANDIOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / S-1,2-PROPANEDIOL / Entry-fusion complex associated protein OPG083
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsDiesterbeck, U.S. / Gittis, A.G. / Garboczi, D.N. / Moss, B.
CitationJournal: Sci Rep / Year: 2018
Title: The 2.1 angstrom structure of protein F9 and its comparison to L1, two components of the conserved poxvirus entry-fusion complex.
Authors: Diesterbeck, U.S. / Gittis, A.G. / Garboczi, D.N. / Moss, B.
History
DepositionFeb 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Protein F9
B: Protein F9
C: Protein F9
D: Protein F9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,217183
Polymers78,5434
Non-polymers13,675179
Water3,891216
1
A: Protein F9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,16452
Polymers19,6361
Non-polymers3,52851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein F9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,26937
Polymers19,6361
Non-polymers2,63336
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein F9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,06043
Polymers19,6361
Non-polymers3,42442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein F9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,72551
Polymers19,6361
Non-polymers4,08950
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.450, 75.080, 136.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Protein F9


Mass: 19635.631 Da / Num. of mol.: 4 / Fragment: residues 1-176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus (strain Western Reserve)
Strain: Western Reserve / Gene: VACWR048, F9L / Production host: Escherichia coli (E. coli) / References: UniProt: P24361

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Non-polymers , 15 types, 395 molecules

#2: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: precipitant*YM
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O2
#8: Chemical...
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 47 / Source method: obtained synthetically / Formula: C2H6O
#9: Chemical...
ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: CH4O
#10: Chemical
ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O2
#11: Chemical
ChemComp-ETX / 2-ETHOXYETHANOL


Mass: 90.121 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O2
#12: Chemical ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H20O5
#13: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#14: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#15: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Crystals were grown from a solution containing 25% PEG 8000, 10% ethanol, 1-5% cocktail mixture of low molecular alcohols, 30% sucrose at pH 8.5 buffered with Tris in the presence of 50mM ...Details: Crystals were grown from a solution containing 25% PEG 8000, 10% ethanol, 1-5% cocktail mixture of low molecular alcohols, 30% sucrose at pH 8.5 buffered with Tris in the presence of 50mM NaCl. The protein concentration was 10mg/ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Nov 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→38.86 Å / Num. obs: 37485 / % possible obs: 93.83 % / Redundancy: 8.7 % / Net I/σ(I): 7.5
Reflection shellResolution: 2.1→2.15 Å / Num. unique obs: 1884 / % possible all: 67

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→38.86 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 32.59
RfactorNum. reflection% reflection
Rfree0.2685 2000 5.34 %
Rwork0.2257 --
obs0.2279 37485 93.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→38.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4927 0 898 216 6041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145744
X-RAY DIFFRACTIONf_angle_d1.7287377
X-RAY DIFFRACTIONf_dihedral_angle_d18.6051955
X-RAY DIFFRACTIONf_chiral_restr0.06818
X-RAY DIFFRACTIONf_plane_restr0.02895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15250.38171010.35181783X-RAY DIFFRACTION67
2.1525-2.21070.35651130.31472017X-RAY DIFFRACTION75
2.2107-2.27570.36651250.2942223X-RAY DIFFRACTION84
2.2757-2.34910.28661370.26572429X-RAY DIFFRACTION91
2.3491-2.43310.30261500.26952653X-RAY DIFFRACTION98
2.4331-2.53050.3061470.25412627X-RAY DIFFRACTION99
2.5305-2.64560.36441500.26142659X-RAY DIFFRACTION99
2.6456-2.78510.3461510.2382672X-RAY DIFFRACTION99
2.7851-2.95950.24941510.23492684X-RAY DIFFRACTION100
2.9595-3.18790.27171510.22482683X-RAY DIFFRACTION100
3.1879-3.50860.24431530.20082701X-RAY DIFFRACTION100
3.5086-4.01580.20611530.19412728X-RAY DIFFRACTION100
4.0158-5.05770.22911570.18382769X-RAY DIFFRACTION100
5.0577-38.86670.26861610.22682857X-RAY DIFFRACTION99

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