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- PDB-4heo: Hendra virus Phosphoprotein C terminal domain -

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Basic information

Entry
Database: PDB / ID: 4heo
TitleHendra virus Phosphoprotein C terminal domain
ComponentsPhosphoprotein
KeywordsVIRAL PROTEIN / viral polymerase cofactor / Phosphoprotein
Function / homology
Function and homology information


disordered domain specific binding / amyloid fibril formation / protein-containing complex
Similarity search - Function
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 / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 ...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 / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHendra virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsYabukarski, F. / Tarbouriech, N. / Jamin, M.
CitationJournal: Plos Pathog. / Year: 2013
Title: Atomic Resolution Description of the Interaction between the Nucleoprotein and Phosphoprotein of Hendra Virus.
Authors: Communie, G. / Habchi, J. / Yabukarski, F. / Blocquel, D. / Schneider, R. / Tarbouriech, N. / Papageorgiou, N. / Ruigrok, R.W. / Jamin, M. / Jensen, M.R. / Longhi, S. / Blackledge, M.
History
DepositionOct 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoprotein
B: Phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3984
Polymers15,3382
Non-polymers602
Water63135
1
A: Phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7042
Polymers7,6691
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6932
Polymers7,6691
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)21.490, 43.280, 51.260
Angle α, β, γ (deg.)90.00, 79.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphoprotein / Protein P


Mass: 7668.996 Da / Num. of mol.: 2 / Fragment: C terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hendra virus / Strain: horse/Australia/Hendra/1994 / Gene: P/V/C / Plasmid: pet28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: O55778
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Bis-Tris 100mM, PEG 3350 28%, MgCl2 50mM, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2012
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.65→32.85 Å / Num. all: 21848 / Num. obs: 21541 / % possible obs: 98.6 % / Redundancy: 2.7 % / Biso Wilson estimate: 34.39 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 14.24
Reflection shellResolution: 1.65→1.8 Å / Redundancy: 2.48 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 1.89 / Num. unique all: 4965 / % possible all: 98.7

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Processing

Software
NameVersionClassification
DNAdata collection
HKL2Mapmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XDSdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→32.848 Å / SU ML: 0.23 / σ(F): 1.23 / Phase error: 23.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2235 1217 5.65 %RANDOM
Rwork0.1881 ---
obs0.1901 21540 98.64 %-
all-21848 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.419 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.0467 Å20 Å20.519 Å2
2--0.826 Å20 Å2
3---2.2208 Å2
Refinement stepCycle: LAST / Resolution: 1.65→32.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms933 0 2 35 970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012986
X-RAY DIFFRACTIONf_angle_d1.1171335
X-RAY DIFFRACTIONf_dihedral_angle_d15.826400
X-RAY DIFFRACTIONf_chiral_restr0.069158
X-RAY DIFFRACTIONf_plane_restr0.004179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.71610.30581400.30582181X-RAY DIFFRACTION98
1.7161-1.79420.32581190.28712368X-RAY DIFFRACTION100
1.7942-1.88880.24931230.22492230X-RAY DIFFRACTION100
1.8888-2.00710.22931440.19462307X-RAY DIFFRACTION100
2.0071-2.1620.20641320.17262324X-RAY DIFFRACTION100
2.162-2.37960.22681280.16942260X-RAY DIFFRACTION100
2.3796-2.72370.19931510.18382254X-RAY DIFFRACTION99
2.7237-3.4310.21461510.17742242X-RAY DIFFRACTION98
3.431-32.85430.22391290.18142157X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3480.8335-0.82031.8101-1.64921.4844-0.0833-0.08830.06130.03130.1322-0.3337-0.08680.04370.00020.16660.0012-0.02930.2337-0.01050.19418.472613.963140.3817
21.5567-1.15-0.331.6112-0.14121.61340.125-0.1037-0.27290.38330.0307-0.4330.509-0.1101-0.05150.2892-0.0034-0.06340.25760.07730.203917.48868.188347.029
31.46280.44960.76160.3086-0.12711.1935-0.3859-0.47940.10370.2941-0.15790.892-0.101-0.0267-0.0390.24050.02320.01480.3202-0.00380.28798.691914.073444.3302
40.99630.07580.13341.4306-1.66011.9370.00520.0718-0.1794-0.1817-0.15650.20170.26570.3123-0.00340.1485-0.0115-0.01650.18430.03290.19769.40615.675632.9189
51.3836-0.1250.31131.1031-0.71022.58460.07470.1302-0.0716-0.451-0.06050.40150.0784-0.1-0.01030.1720.01070.00480.15320.09930.22578.67523.362727.5279
61.2889-0.48910.99150.9416-0.77790.91740.0766-0.23281.10010.08230.0728-0.4603-0.21690.6098-0.02440.1733-0.00810.00670.22530.00970.344916.930522.623134.0877
70.66670.1452-0.56540.0353-0.12230.4917-0.12940.6349-1.29090.0843-0.4256-0.19330.6199-0.0154-0.10090.8830.154-0.32290.3535-0.38851.141513.320427.403650.5891
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:19)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 20:38)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 39:56)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 2:19)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 20:38)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 39:55)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 56:60)

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