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- PDB-5wco: Matrix Protein (M1) of Infectious Salmon Anaemia Virus -

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Basic information

Entry
Database: PDB / ID: 5wco
TitleMatrix Protein (M1) of Infectious Salmon Anaemia Virus
ComponentsNS2
KeywordsVIRAL PROTEIN / Matrix protein / ISAV / Orthomyxovirus / helical
Function / homologyNS2
Function and homology information
Biological speciesInfectious salmon anemia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.604 Å
AuthorsZhang, W. / Zheng, W. / Toh, Y. / Betancourt, M.A. / Tu, J. / Fan, Y. / Vakharia, V. / Liu, J. / McNew, J.A. / Jin, M. / Tao, Y.J.
Funding support United States, 2items
OrganizationGrant numberCountry
Welch FoundationC-1565 to YJT United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI077785 to YJT United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Crystal structure of an orthomyxovirus matrix protein reveals mechanisms for self-polymerization and membrane association.
Authors: Zhang, W. / Zheng, W. / Toh, Y. / Betancourt-Solis, M.A. / Tu, J. / Fan, Y. / Vakharia, V.N. / Liu, J. / McNew, J.A. / Jin, M. / Tao, Y.J.
History
DepositionJul 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NS2
B: NS2
C: NS2


Theoretical massNumber of molelcules
Total (without water)72,5113
Polymers72,5113
Non-polymers00
Water27015
1
A: NS2


Theoretical massNumber of molelcules
Total (without water)24,1701
Polymers24,1701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NS2


Theoretical massNumber of molelcules
Total (without water)24,1701
Polymers24,1701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NS2


Theoretical massNumber of molelcules
Total (without water)24,1701
Polymers24,1701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.799, 95.886, 85.410
Angle α, β, γ (deg.)90.000, 93.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NS2 / Non-structural protein 2 / ORF1


Mass: 24170.395 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Infectious salmon anemia virus / Gene: NS2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q910W0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.19 Å3/Da / Density % sol: 43.78 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.5
Details: 3 uL protein solution (20 mg/mL M1 protein in 200 mM sodium chloride, 10% glycerol, 25 mM Tris-HCl, pH 7.5) + 1 uL mother liquor (0.2 M sodium chloride, 14% PEG3350, 0.1 M Bis-Tris, pH 6.5)

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 21-ID-G10.97856
SYNCHROTRONAPS 21-ID-F20.97872
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDApr 11, 2014
MARMOSAIC 225 mm CCD2CCDAug 18, 2014
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1diamond(111)SINGLE WAVELENGTHMx-ray1
2diamond(111)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978561
20.978721
ReflectionResolution: 2.6→50 Å / Num. obs: 18884 / % possible obs: 98.5 % / Redundancy: 4.7 % / Biso Wilson estimate: 56.64 Å2 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.046 / Rrim(I) all: 0.102 / Χ2: 1.006 / Net I/σ(I): 9.4 / Num. measured all: 88204
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.6440.8269230.7230.4580.9470.8498.2
2.64-2.694.30.6599170.7590.3510.7490.80898.2
2.69-2.744.60.6299640.8420.3230.7080.90397.8
2.74-2.84.70.6099320.8530.3060.6830.92398
2.8-2.864.80.5039210.8830.2490.5620.92698.5
2.86-2.934.80.4069510.9210.2010.4541.01898.2
2.93-34.80.3539350.9510.1750.3951.0198.5
3-3.084.80.2969420.960.1460.331.0298.8
3.08-3.174.80.2369260.9730.1170.2641.08898.2
3.17-3.284.80.2069600.9720.1020.2311.09199
3.28-3.394.80.1549350.9840.0760.1721.06898.7
3.39-3.534.80.1249700.990.0620.1391.04398.4
3.53-3.694.80.1059260.9920.0520.1181.07999.5
3.69-3.884.70.0889500.9940.0450.0991.08798.4
3.88-4.134.80.0779380.9930.0380.0861.02499.3
4.13-4.454.70.0699410.9960.0350.0781.00898.6
4.45-4.894.70.0599620.9960.030.0661.10698.7
4.89-5.64.70.0569660.9980.0280.0631.03799.2
5.6-7.054.70.0569500.9960.0280.0631.01699.3
7.05-504.50.0439750.9980.0210.0480.94697.6

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Phasing

PhasingMethod: SIRAS
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-2.01821.797-1.767AU187.691
20.2321.87622.434AU135.821.2
336.94225.39232.249AU3000.52
433.90721.87446.501AU139.451.07
522.1578.28917.733AU3000.81

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
SHARPphasing
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SIRAS / Resolution: 2.604→28.053 Å / FOM work R set: 0.7662 / SU ML: 0.36 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 30.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2527 921 4.89 %
Rwork0.2026 17917 -
obs0.2052 18838 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.12 Å2 / Biso mean: 65.18 Å2 / Biso min: 30.91 Å2
Refinement stepCycle: final / Resolution: 2.604→28.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4569 0 0 15 4584
Biso mean---52.37 -
Num. residues----588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014648
X-RAY DIFFRACTIONf_angle_d1.5856242
X-RAY DIFFRACTIONf_chiral_restr0.104701
X-RAY DIFFRACTIONf_plane_restr0.006783
X-RAY DIFFRACTIONf_dihedral_angle_d17.2061825
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6037-2.74080.32791190.23782501262096
2.7408-2.91240.36321190.23432531265098
2.9124-3.1370.30141310.22992583271499
3.137-3.45220.32141300.22392552268299
3.4522-3.95050.20451390.19052583272299
3.9505-4.97270.21291300.18132575270599
4.9727-28.05470.2511530.19942592274598

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