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- PDB-2fqm: Crystal structure of the oligomerization domain of the phosphopro... -

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Basic information

Entry
Database: PDB / ID: 2fqm
TitleCrystal structure of the oligomerization domain of the phosphoprotein of vesicular stomatitis virus
ComponentsPhosphoprotein
KeywordsVIRAL PROTEIN / negative strand RNA virus / polymerase / replication / cofactor
Function / homology
Function and homology information


virion component / host cell cytoplasm / RNA-directed RNA polymerase activity
Similarity search - Function
Helix Hairpins - #830 / Phosphoprotein, central domain / : / Vesiculovirus phosphoprotein / Phosphoprotein, C-terminal domain, viral / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Biological speciesVesicular stomatitis Indiana virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsDing, H. / Green, T.J. / Lu, S. / Luo, M.
CitationJournal: J.Virol. / Year: 2006
Title: Crystal structure of the oligomerization domain of the phosphoprotein of vesicular stomatitis virus
Authors: Ding, H. / Green, T.J. / Lu, S. / Luo, M.
History
DepositionJan 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoprotein
B: Phosphoprotein
C: Phosphoprotein
D: Phosphoprotein
E: Phosphoprotein
F: Phosphoprotein


Theoretical massNumber of molelcules
Total (without water)50,6556
Polymers50,6556
Non-polymers00
Water1,51384
1
A: Phosphoprotein
B: Phosphoprotein


Theoretical massNumber of molelcules
Total (without water)16,8852
Polymers16,8852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-31 kcal/mol
Surface area7770 Å2
MethodPISA
2
C: Phosphoprotein
D: Phosphoprotein


Theoretical massNumber of molelcules
Total (without water)16,8852
Polymers16,8852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-35 kcal/mol
Surface area8580 Å2
MethodPISA
3
E: Phosphoprotein
F: Phosphoprotein


Theoretical massNumber of molelcules
Total (without water)16,8852
Polymers16,8852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-32 kcal/mol
Surface area8530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.380, 74.380, 157.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a dimer composed of molecule A and B.

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Components

#1: Protein
Phosphoprotein / P protein


Mass: 8442.568 Da / Num. of mol.: 6 / Mutation: L139M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vesicular stomatitis Indiana virus / Genus: Vesiculovirus / Strain: Indiana / Gene: P / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04880
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.15 Å3/Da / Density % sol: 42.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.32
Details: 2.48 M ammonium sulfate, 7% ethylene glycol, 0.05% n-octyl-b-D-glucopyranoside, pH 4.32, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9792 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 8, 2005
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 20435 / Num. obs: 20381 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 22.62
Reflection shellHighest resolution: 2.3 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: SAD / Resolution: 2.3→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 983 5 %random
Rwork0.225 ---
all0.227 20108 --
obs0.227 20108 98.8 %-
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3193 0 0 84 3277
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.026
X-RAY DIFFRACTIONx_angle_deg2.263

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