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- PDB-3l32: Structure of the dimerisation domain of the rabies virus phosphop... -

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Basic information

Entry
Database: PDB / ID: 3l32
TitleStructure of the dimerisation domain of the rabies virus phosphoprotein
ComponentsPhosphoprotein
KeywordsVIRAL PROTEIN / antiparallel alpha-helices / dimerisation domain / rabies virus / phosphoprotein
Function / homology
Function and homology information


virion component => GO:0044423 / microtubule-dependent intracellular transport of viral material towards nucleus / viral transcription / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / RNA-dependent RNA polymerase activity / host cell nucleus
Similarity search - Function
Helix Hairpins - #1560 / Phosphoprotein / Phosphoprotein, C-terminal / Phosphoprotein / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Biological speciesRabies virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsIvanov, I. / Crepin, T. / Jamin, M. / Ruigrok, R.W.H.
CitationJournal: J.Virol. / Year: 2010
Title: Structure of the dimerisation domain of the rabies virus phosphoprotein
Authors: Ivanov, I. / Crepin, T. / Jamin, M. / Ruigrok, R.W.H.
History
DepositionDec 16, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoprotein
B: Phosphoprotein


Theoretical massNumber of molelcules
Total (without water)10,6862
Polymers10,6862
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-21 kcal/mol
Surface area5670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.290, 43.290, 192.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein/peptide Phosphoprotein / Protein P / Protein M1


Mass: 5343.142 Da / Num. of mol.: 2 / Fragment: UNP residues 90-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rabies virus / Strain: China/MRV / Gene: P / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q0GBY3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.1 Å3/Da / Density % sol: 41.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: (NH4)2SO4, pH 6.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-410.976
SYNCHROTRONESRF BM1421.771
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDJul 28, 2009
MAR scanner 345 mm plate2IMAGE PLATESep 25, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9761
21.7711
ReflectionResolution: 1.5→25.81 Å / Num. obs: 15278 / Redundancy: 7.6 % / Rmerge(I) obs: 0.047

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.5→25.81 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.307 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22811 759 5 %RANDOM
Rwork0.19647 ---
obs0.19796 14377 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.388 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2---0.29 Å20 Å2
3---0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.5→25.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms760 0 0 51 811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.022777
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4931.9291058
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.974597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.9552440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.58415143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.722156
X-RAY DIFFRACTIONr_chiral_restr0.1730.2124
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02580
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7551.5454
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.2052750
X-RAY DIFFRACTIONr_scbond_it4.4513323
X-RAY DIFFRACTIONr_scangle_it7.6134.5303
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 50 -
Rwork0.245 1059 -
obs--99.91 %

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