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- PDB-4xyp: Crystal structure of a piscine viral fusion protein -

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Basic information

Entry
Database: PDB / ID: 4xyp
TitleCrystal structure of a piscine viral fusion protein
ComponentsFusion protein
KeywordsVIRAL PROTEIN / heptad repeat / 6-helix bundle / class I viral fusion protein
Function / homologyFusion glycoprotein F0, Isavirus / Fusion glycoprotein F0, Isavirus / membrane => GO:0016020 / 3,7-BIS(DIMETHYLAMINO)PHENOTHIAZIN-5-IUM / Fusion protein / Fusion protein
Function and homology information
Biological speciesInfectious salmon anemia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsCook, J.D. / Lee, J.E.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN435607-13 Canada
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Electrostatic Architecture of the Infectious Salmon Anemia Virus (ISAV) Core Fusion Protein Illustrates a Carboxyl-Carboxylate pH Sensor.
Authors: Cook, J.D. / Soto-Montoya, H. / Korpela, M.K. / Lee, J.E.
History
DepositionFeb 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Aug 5, 2015Group: Database references / Other
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2674
Polymers7,9121
Non-polymers3553
Water1086
1
A: Fusion protein
hetero molecules

A: Fusion protein
hetero molecules

A: Fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,80212
Polymers23,7363
Non-polymers1,0669
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area9050 Å2
ΔGint-111 kcal/mol
Surface area12120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.874, 42.874, 232.245
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-402-

CL

21A-403-

CL

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Components

#1: Protein Fusion protein /


Mass: 7912.075 Da / Num. of mol.: 1 / Fragment: UNP residues 156-225
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Infectious salmon anemia virus / Plasmid: pET46 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: V5RD79, UniProt: C6F339*PLUS
#2: Chemical ChemComp-MBT / 3,7-BIS(DIMETHYLAMINO)PHENOTHIAZIN-5-IUM / METHYLENE BLUE / Methylene blue


Mass: 284.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18N3S / Comment: medication*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.6 Å3/Da / Density % sol: 52.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1:1 volume ratio of 30mg/mL protein solution and 0.2 M lithium sulfate, 0.1 M sodium acetate, pH 4.5, 2 mg/mL tetramethylthionine chloride and 50% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 14, 2013 / Details: 9 CCDs, 9 tiled fiber-optic tapers
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.1→38.71 Å / Num. obs: 5037 / % possible obs: 97.6 % / Redundancy: 4.7 % / Biso Wilson estimate: 33.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.032 / Net I/σ(I): 13.7 / Num. measured all: 23796
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.1-2.1640.4953.214533610.8330.24788.6
8.92-38.713.70.03627.8325870.9990.02393.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.1 Å38.71 Å
Translation2.1 Å38.71 Å

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Processing

Software
NameVersionClassification
PHASER2.5.3phasing
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
Aimless0.1.27data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→38.707 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 23.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2511 503 10 %Random selection
Rwork0.1958 4527 --
obs0.201 5030 97.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.88 Å2 / Biso mean: 45.5257 Å2 / Biso min: 23.55 Å2
Refinement stepCycle: final / Resolution: 2.1→38.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms529 0 22 6 557
Biso mean--36.85 47.95 -
Num. residues----70
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011560
X-RAY DIFFRACTIONf_angle_d1.234762
X-RAY DIFFRACTIONf_chiral_restr0.05491
X-RAY DIFFRACTIONf_plane_restr0.00696
X-RAY DIFFRACTIONf_dihedral_angle_d16.676198
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.31470.24411210.17061088120996
2.3147-2.64960.21731250.15711271252100
2.6496-3.33790.24191260.18891130125699
3.3379-38.7140.26711310.2151182131396

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