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- PDB-4n5b: Crystal structure of the Nipah virus phosphoprotein tetramerizati... -

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Basic information

Entry
Database: PDB / ID: 4n5b
TitleCrystal structure of the Nipah virus phosphoprotein tetramerization domain
ComponentsPhosphoprotein
KeywordsVIRAL PROTEIN / Viral Polymerase Co-Factor / Nucleoprotein Chaperone / Interferon Inhibitor
Function / homology
Function and homology information


Phosphoprotein P region PNT disordered / Phosphoprotein P region PNT disordered / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal
Similarity search - Domain/homology
IMIDAZOLE / Phosphoprotein
Similarity search - Component
Biological speciesNipah virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.2 Å
AuthorsBruhn, J.F. / Barnett, K. / Bibby, J. / Thomas, J. / Keegan, R. / Rigden, D. / Bornholdt, Z.A. / Saphire, E.O.
CitationJournal: J.Virol. / Year: 2014
Title: Crystal structure of the nipah virus phosphoprotein tetramerization domain.
Authors: Bruhn, J.F. / Barnett, K.C. / Bibby, J. / Thomas, J.M. / Keegan, R.M. / Rigden, D.J. / Bornholdt, Z.A. / Saphire, E.O.
History
DepositionOct 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoprotein
E: Phosphoprotein
D: Phosphoprotein
C: Phosphoprotein
H: Phosphoprotein
F: Phosphoprotein
B: Phosphoprotein
G: Phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,42929
Polymers100,9798
Non-polymers1,45121
Water15,493860
1
A: Phosphoprotein
D: Phosphoprotein
C: Phosphoprotein
B: Phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,24915
Polymers50,4894
Non-polymers76011
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21310 Å2
ΔGint-165 kcal/mol
Surface area19750 Å2
MethodPISA
2
E: Phosphoprotein
H: Phosphoprotein
F: Phosphoprotein
G: Phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,18014
Polymers50,4894
Non-polymers69110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22160 Å2
ΔGint-162 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.061, 76.877, 80.748
Angle α, β, γ (deg.)100.56, 100.85, 107.78
Int Tables number1
Space group name H-MP1
DetailsChains A, B, C and D / Chains E, F, G and H

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Components

#1: Protein
Phosphoprotein


Mass: 12622.337 Da / Num. of mol.: 8 / Fragment: Tetramerization Domain residues 470-578
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nipah virus / Strain: Ind-Nipah-07-FG / Gene: P/V/W/C / Plasmid: pET46 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: D2DEB8
#2: Chemical...
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 860 / 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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M imidazole pH 7.0, 25% PEG MME 550, 15% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 100K, temperature 295.5K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2013
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→46.37 Å / Num. obs: 51813 / % possible obs: 97.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.063 / Net I/σ(I): 9.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.85 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 3 / % possible all: 97.2

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Processing

Software
NameVersionClassification
Web-Icedata collection
AMPLEphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: AB INITIO PHASING
Starting model: PDB ENTRY 4EIJ

4eij


Resolution: 2.2→46.369 Å / SU ML: 0.23 / σ(F): 1.97 / Phase error: 27.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 2617 5.06 %RANDOM
Rwork0.1869 ---
obs0.1895 51738 97.59 %-
all-51738 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→46.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6535 0 105 860 7500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036751
X-RAY DIFFRACTIONf_angle_d0.6359089
X-RAY DIFFRACTIONf_dihedral_angle_d13.1112514
X-RAY DIFFRACTIONf_chiral_restr0.0261063
X-RAY DIFFRACTIONf_plane_restr0.0041167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.27531250.23842574X-RAY DIFFRACTION97
2.24-2.28310.2831370.2262578X-RAY DIFFRACTION97
2.2831-2.32970.26311520.21392552X-RAY DIFFRACTION97
2.3297-2.38030.27391300.21132598X-RAY DIFFRACTION97
2.3803-2.43570.2621410.20972576X-RAY DIFFRACTION98
2.4357-2.49660.29451510.21052566X-RAY DIFFRACTION98
2.4966-2.56410.27861300.20582614X-RAY DIFFRACTION98
2.5641-2.63950.26831450.20482553X-RAY DIFFRACTION98
2.6395-2.72470.27851560.19872570X-RAY DIFFRACTION98
2.7247-2.82210.28341340.18392643X-RAY DIFFRACTION98
2.8221-2.93510.26091410.19232561X-RAY DIFFRACTION98
2.9351-3.06860.22631440.20492630X-RAY DIFFRACTION98
3.0686-3.23040.29671400.19572611X-RAY DIFFRACTION98
3.2304-3.43270.27381370.18992618X-RAY DIFFRACTION98
3.4327-3.69770.19971390.17152599X-RAY DIFFRACTION98
3.6977-4.06960.18961220.14322617X-RAY DIFFRACTION98
4.0696-4.6580.18441520.1432517X-RAY DIFFRACTION97
4.658-5.86670.22141160.20142604X-RAY DIFFRACTION97
5.8667-46.37920.24711250.21582540X-RAY DIFFRACTION95

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