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- PDB-4c5q: measles virus phosphoprotein tetramerization domain -

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Basic information

Entry
Database: PDB / ID: 4c5q
Titlemeasles virus phosphoprotein tetramerization domain
ComponentsPHOSPHOPROTEIN
KeywordsVIRAL PROTEIN / OLIGOMERIZATION DOMAIN
Function / homology
Function and homology information


viral genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / RNA binding
Similarity search - Function
RNA polymerase, phosphoprotein P, C-terminal XD, paramyxovirinae / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal
Similarity search - Domain/homology
Biological speciesMEASLES VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBlocquel, D. / Habchi, J. / Durand, E. / Sevajol, M. / Ferron, F. / Papageorgiou, N. / Longhi, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Coiled-Coil Deformations in Crystal Structures: The Measles Virus Phosphoprotein Multimerization Domain as an Illustrative Example.
Authors: Blocquel, D. / Habchi, J. / Durand, E. / Sevajol, M. / Ferron, F. / Erales, J. / Papageorgiou, N. / Longhi, S.
History
DepositionSep 14, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOPROTEIN
B: PHOSPHOPROTEIN
C: PHOSPHOPROTEIN
D: PHOSPHOPROTEIN
E: PHOSPHOPROTEIN
F: PHOSPHOPROTEIN
G: PHOSPHOPROTEIN
H: PHOSPHOPROTEIN


Theoretical massNumber of molelcules
Total (without water)72,4588
Polymers72,4588
Non-polymers00
Water4,756264
1
A: PHOSPHOPROTEIN
B: PHOSPHOPROTEIN
C: PHOSPHOPROTEIN
D: PHOSPHOPROTEIN


Theoretical massNumber of molelcules
Total (without water)36,2294
Polymers36,2294
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9370 Å2
ΔGint-69.7 kcal/mol
Surface area11360 Å2
MethodPISA
2
E: PHOSPHOPROTEIN
F: PHOSPHOPROTEIN
G: PHOSPHOPROTEIN
H: PHOSPHOPROTEIN


Theoretical massNumber of molelcules
Total (without water)36,2294
Polymers36,2294
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9410 Å2
ΔGint-69.1 kcal/mol
Surface area11270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.343, 34.392, 139.693
Angle α, β, γ (deg.)97.04, 96.90, 90.12
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
PHOSPHOPROTEIN / PROTEIN P


Mass: 9057.310 Da / Num. of mol.: 8 / Fragment: TETRAMERIZATION DOMAIN, RESIDUES 304-375 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MEASLES VIRUS / Strain: EDMONSTON B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: P35974
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.24 Å3/Da / Density % sol: 45.17 % / Description: NONE
Crystal growpH: 9.5 / Details: 10% PEG 8000, 0.1 M NACL, 0.1 M CHES, PH 9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97911
DetectorType: PIXEL PILATUS / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.15→45.87 Å / Num. obs: 32947 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.3
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.3 / % possible all: 88.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
PHENIXdata scaling
PHENIXPHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EZJ

1ezj


Resolution: 2.2→34.125 Å / SU ML: 0.33 / σ(F): 1.98 / Phase error: 30.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2949 1569 5 %
Rwork0.2499 --
obs0.2522 31104 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.6 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3403 0 0 264 3667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073421
X-RAY DIFFRACTIONf_angle_d1.0184571
X-RAY DIFFRACTIONf_dihedral_angle_d15.8871355
X-RAY DIFFRACTIONf_chiral_restr0.071548
X-RAY DIFFRACTIONf_plane_restr0.003578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2710.29511480.26662702X-RAY DIFFRACTION97
2.271-2.35220.28041370.27352615X-RAY DIFFRACTION96
2.3522-2.44630.25641430.24262734X-RAY DIFFRACTION97
2.4463-2.55760.25631420.22342636X-RAY DIFFRACTION97
2.5576-2.69240.24711340.21522716X-RAY DIFFRACTION97
2.6924-2.8610.27181410.22952747X-RAY DIFFRACTION98
2.861-3.08180.29591330.22272676X-RAY DIFFRACTION98
3.0818-3.39170.37491480.24152666X-RAY DIFFRACTION98
3.3917-3.88190.28671450.22112722X-RAY DIFFRACTION98
3.8819-4.88850.27671590.23272711X-RAY DIFFRACTION98
4.8885-34.12950.35891390.35852610X-RAY DIFFRACTION95

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