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- PDB-5jie: Crystal structure of the Orsay virus delta protein N-terminal fra... -

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Basic information

Entry
Database: PDB / ID: 5jie
TitleCrystal structure of the Orsay virus delta protein N-terminal fragment (aa 1~66)
ComponentsProtein delta
KeywordsVIRAL PROTEIN / Delta protein / Orsay virus / C. elegans / helical
Function / homologyProtein delta
Function and homology information
Biological speciesOrsay virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1374 Å
AuthorsFan, Y. / Guo, Y. / Zhong, W. / Tao, Y.J.
CitationJournal: PLoS Pathog. / Year: 2017
Title: Structure of a pentameric virion-associated fiber with a potential role in Orsay virus entry to host cells.
Authors: Fan, Y. / Guo, Y.R. / Yuan, W. / Zhou, Y. / Holt, M.V. / Wang, T. / Demeler, B. / Young, N.L. / Zhong, W. / Tao, Y.J.
History
DepositionApr 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Protein delta
C: Protein delta
E: Protein delta
D: Protein delta
A: Protein delta


Theoretical massNumber of molelcules
Total (without water)36,6925
Polymers36,6925
Non-polymers00
Water3,549197
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14500 Å2
ΔGint-142 kcal/mol
Surface area14830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.013, 32.133, 65.648
Angle α, β, γ (deg.)90.000, 99.710, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Protein delta


Mass: 7338.308 Da / Num. of mol.: 5 / Fragment: UNP residues 1-66
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orsay virus / Production host: Escherichia coli (E. coli) / References: UniProt: E9KNV6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.4850.39
2
Crystal grow
Temperature (K)Crystal-IDMethodDetails
2931vapor diffusion, hanging drop1.6 M ammonium sulfate, 0.1 M MES monohydrate (pH 6.5), and 12% v/v dioxane
2932evaporation0.1 M citric acid (pH 5.0) and 14% (w/v) PEG 6,000

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 21-ID-D10.97853
SYNCHROTRONAPS 21-ID-G20.97857
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDFeb 12, 2015
MARMOSAIC 300 mm CCD2CCDApr 3, 2015
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978531
20.978571
ReflectionResolution: 2.137→50 Å / Num. obs: 19535 / % possible obs: 95.9 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.122 / Net I/av σ(I): 11.738 / Net I/σ(I): 6.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.137-2.183.40.583176.5
2.18-2.223.50.508181.8
2.22-2.263.70.437185.1
2.26-2.313.70.423190.1
2.31-2.363.90.405193
2.36-2.4140.378195.3
2.41-2.474.20.381197.6
2.47-2.544.40.356199
2.54-2.614.50.3321100
2.61-2.74.60.261100
2.7-2.794.70.2461100
2.79-2.94.80.2241100
2.9-3.044.70.1851100
3.04-3.24.70.1521100
3.2-3.44.60.1131100
3.4-3.664.60.089199.8
3.66-4.034.60.082199.9
4.03-4.614.50.061199.9
4.61-5.814.50.0531100
5.81-504.30.049199.3

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
AutoSolphasing
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.1374→48.018 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.57
RfactorNum. reflection% reflection
Rfree0.2314 953 4.88 %
Rwork0.2064 --
obs0.2077 19510 95.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.72 Å2 / Biso mean: 35.3721 Å2 / Biso min: 18.84 Å2
Refinement stepCycle: final / Resolution: 2.1374→48.018 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 0 197 2493
Biso mean---41.22 -
Num. residues----294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082338
X-RAY DIFFRACTIONf_angle_d0.8463184
X-RAY DIFFRACTIONf_chiral_restr0.044381
X-RAY DIFFRACTIONf_plane_restr0.005387
X-RAY DIFFRACTIONf_dihedral_angle_d13.682818
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1374-2.25010.2725950.23472128222378
2.2501-2.3910.24961340.21482504263892
2.391-2.57570.25551390.21582701284098
2.5757-2.83480.26271410.200227812922100
2.8348-3.24490.22741590.198727632922100
3.2449-4.0880.231370.188828102947100
4.088-48.030.2071480.21632870301899

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