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- PDB-4hiy: crystal structure of R34/53A, D95N, H112W mutant of borna disease... -

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Basic information

Entry
Database: PDB / ID: 4hiy
Titlecrystal structure of R34/53A, D95N, H112W 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
Biological speciesBorna disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 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)16,2492
Polymers16,1531
Non-polymers961
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
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)64,9958
Polymers64,6114
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation20_555x,-z,y1
Buried area8940 Å2
ΔGint-89 kcal/mol
Surface area24470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.417, 137.417, 137.417
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: 16152.665 Da / Num. of mol.: 1 / Mutation: R34A, R53A, D95N, H112W
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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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: 3.35 Å3/Da / Density % sol: 63.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.125 Li2SO4, 25% GLYCEROL, 0.075 HEPES, 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 Å
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→56 Å / Num. all: 3517 / Num. obs: 3517 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 11.2 % / Biso Wilson estimate: 70 Å2 / Rmerge(I) obs: 0.155 / Net I/σ(I): 11.9
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.789 / Mean I/σ(I) obs: 3.2 / Num. unique all: 493 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3F1J

3f1j


Resolution: 3.31→56 Å / Cor.coef. Fo:Fc: 0.94 / SU B: 14.355 / SU ML: 0.233 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / 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: R VALUE (WORKING SET) = 0.175; FREE R = 0. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. STRUCTURE SOLUTION AND REFINEMENT WERE PERFORMED USING FREE R FOR CROSS-VALIDATION THROUGHOUT: R VALUE (WORKING SET) = 0.175; FREE R = 0.233 FROM A RANDOM TEST SET COMPRISING 5% OF REFLECTIONS (157 TOTAL). FINAL REFINEMENT WAS PERFORMED USING ALL REFLECTIONS.
RfactorNum. reflection% reflectionSelection details
Rwork0.1749 ---
obs0.1807 3515 99 %-
all-3517 --
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: 64.838 Å2
Refinement stepCycle: LAST / Resolution: 3.31→56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1077 0 5 0 1082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021109
X-RAY DIFFRACTIONr_bond_other_d0.0010.02762
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.9811505
X-RAY DIFFRACTIONr_angle_other_deg0.87531861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8825131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6224.08249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.57815190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.432155
X-RAY DIFFRACTIONr_chiral_restr0.0720.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211194
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02227
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

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