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- PDB-4hi5: crystal structure of F37A mutant of borna disease virus matrix protein -

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Basic information

Entry
Database: PDB / ID: 4hi5
Titlecrystal structure of F37A mutant of borna disease virus matrix protein
ComponentsMatrix proteinViral matrix protein
KeywordsVIRAL PROTEIN / VIRAL MATRIX PROTEIN / RNA BINDING / MEMBRANE BINDING / VIRUSES / SSRNA NEGATIVE-STRAND VIRUSES / MONONEGAVIRALES / BORNAVIRIDAE / BORNAVIRUS / VIRION
Function / homology
Function and homology information


virion component / host cell cytoplasm / structural constituent of virion / host cell plasma membrane / membrane / identical protein binding
Similarity search - Function
Borna disease virus, matrix protein / Matrix protein, Bornaviridae / Matrix protein superfamily / ssRNA-binding matrix protein of Bornaviridae / Topoisomerase I; domain 3 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
CYTIDINE-5'-MONOPHOSPHATE / Matrix protein
Similarity search - Component
Biological speciesBorna disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsDautel, P. / Kolenko, P. / Stubbs, M.T.
CitationJournal: To be Published
Title: Matrix protein variants provide support for alternative borna disease virus infection pathway
Authors: Dautel, P. / Kolenko, P. / Stubbs, M.T.
History
DepositionOct 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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

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Assembly

Deposited unit
A: Matrix protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5252
Polymers16,2021
Non-polymers3231
Water0
1
A: Matrix protein
hetero molecules

A: Matrix protein
hetero molecules

A: Matrix protein
hetero molecules

A: Matrix protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1008
Polymers64,8074
Non-polymers1,2934
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
Buried area11090 Å2
ΔGint-33 kcal/mol
Surface area24450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.637, 139.637, 139.637
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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Components

#1: Protein Matrix protein / Viral matrix protein / gp18 / p16


Mass: 16201.722 Da / Num. of mol.: 1 / Mutation: F37A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borna disease virus / Gene: M / Plasmid: PMAL-C2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0C794
#2: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE / Cytidine monophosphate


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P

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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: 3.5 Å3/Da / Density % sol: 64.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.2 M MgCl2, 30% w/v PEG400, 0.1 M HEPES, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 10, 2010 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 3.6→70 Å / Num. obs: 2918 / % possible obs: 100 % / Observed criterion σ(I): -3.7 / Redundancy: 11 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 13.4

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3F1J

3f1j


Resolution: 3.6→70 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.87 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.775 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. STRUCTURE SOLUTION AND REFINEMENT WERE PERFORMED USING FREE R FOR CROSS-VALIDATION THROUGHOUT: WORKING R = 0.2352; FREE R = 0.3125 FROM A ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. STRUCTURE SOLUTION AND REFINEMENT WERE PERFORMED USING FREE R FOR CROSS-VALIDATION THROUGHOUT: WORKING R = 0.2352; FREE R = 0.3125 FROM A RANDOM TEST SET COMPRISING 10% OF ALL REFLECTIONS (273 TOTAL). FINAL REFINEMENT WAS PERFORMED USING ALL REFLECTIONS.
RfactorNum. reflection% reflectionSelection details
obs0.2477 2918 100 %-
all-2918 --
Rfree---RANDOM
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 105.14 Å2
Refinement stepCycle: LAST / Resolution: 3.6→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1095 0 21 0 1116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221144
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0082.0061554
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2615133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.342450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.84915198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.389156
X-RAY DIFFRACTIONr_chiral_restr0.0640.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021847
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_it0.2311.5677
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.41921105
X-RAY DIFFRACTIONr_scbond_it0.2663467
X-RAY DIFFRACTIONr_scangle_it0.4914.5449
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.601→3.694 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.401 -
Rwork0.328 191

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