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- PDB-4hiu: Crystal structure of R34/53A mutant of borna disease virus matrix... -

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Basic information

Entry
Database: PDB / ID: 4hiu
TitleCrystal structure of R34/53A mutant of borna disease virus matrix protein
ComponentsMatrix protein
KeywordsVIRAL PROTEIN / VIRAL MATRIX PROTEIN / RNA BINDING / MEMBRANE BINDING / VIRUSES / SSRNA / NEGATIVE-STRAND VIRUSES / MONONEGAVIRALES / BORNAVIRIDAE / BORNA VIRUS / VIRION
Function / homology
Function and homology information


virion component / structural constituent of virion / host cell cytoplasm / host cell plasma membrane / identical protein binding / membrane
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
GUANOSINE-5'-MONOPHOSPHATE / CYTIDINE-5'-MONOPHOSPHATE / Matrix protein
Similarity search - Component
Biological speciesBorna disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 12, 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)16,7923
Polymers16,1061
Non-polymers6862
Water00
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)67,16812
Polymers64,4224
Non-polymers2,7468
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation23_555-z,y,x1
Buried area11350 Å2
ΔGint-37 kcal/mol
Surface area22300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.732, 139.732, 139.732
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 / gp18 / p16


Mass: 16105.587 Da / Num. of mol.: 1 / Mutation: R34A, R53A
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


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P
#3: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P

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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: 3.53 Å3/Da / Density % sol: 65.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.09 M NPS buffer, 30% GLYCEROL, PEG4000, 0.1 M HEPES (MOPS), pH 7.5, 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: 3.3→50 Å / Num. obs: 3751 / % possible obs: 100 % / Observed criterion σ(I): -3.7 / Redundancy: 11 % / Biso Wilson estimate: 93 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 25.5
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.6.0116refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3F1J

3f1j


Resolution: 3.3→50 Å / Cor.coef. Fo:Fc: 0.935 / SU B: 14.243 / SU ML: 0.229 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rwork0.185 ---
obs0.187 3736 99.8 %-
all-3751 --
Rfree---RANDOM
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.69 Å2
Refinement stepCycle: LAST / Resolution: 3.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1078 0 45 0 1123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221153
X-RAY DIFFRACTIONr_bond_other_d0.0030.02780
X-RAY DIFFRACTIONr_angle_refined_deg1.4742.0291571
X-RAY DIFFRACTIONr_angle_other_deg1.0063.0141911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5155130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.33224.250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.13615195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.334155
X-RAY DIFFRACTIONr_chiral_restr0.0910.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211208
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02226
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.303→3.388 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.279 233

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