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- PDB-4hit: Crystal structure of H112W mutant of borna disease virus matrix p... -

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Basic information

Entry
Database: PDB / ID: 4hit
TitleCrystal structure of 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: 2.4 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
Revision 1.2Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Matrix protein
D: Matrix protein
C: Matrix protein
B: Matrix protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,23915
Polymers65,3044
Non-polymers93511
Water2,450136
1
A: Matrix protein
D: Matrix protein
C: Matrix protein
B: Matrix protein
hetero molecules

A: Matrix protein
D: Matrix protein
C: Matrix protein
B: Matrix protein
hetero molecules

A: Matrix protein
D: Matrix protein
C: Matrix protein
B: Matrix protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,71745
Polymers195,91112
Non-polymers2,80633
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area41570 Å2
ΔGint-589 kcal/mol
Surface area62450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.322, 123.322, 113.501
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
Matrix protein / gp18 / p16


Mass: 16325.882 Da / Num. of mol.: 4 / Mutation: 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 3.82 Å3/Da / Density % sol: 67.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.0 M AMMONIUM SULPHATE, 0.1 M TRIS-HCL, pH 8.5, 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: 2.4→50 Å / Num. all: 37880 / Num. obs: 37880 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 6.9 % / Biso Wilson estimate: 56 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 26.2
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.2 / Num. unique all: 5105 / % possible all: 92.4

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Processing

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

3f1j


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.952 / SU B: 4.966 / SU ML: 0.118 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ALL REFLECTIONS HAVE BEEN USED DURING LAST REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rwork0.1924 ---
all0.1958 37880 --
obs0.1958 37867 98.73 %-
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: 42.957 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å20.85 Å20 Å2
2--1.7 Å20 Å2
3----2.56 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4284 0 47 136 4467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.024448
X-RAY DIFFRACTIONr_bond_other_d0.0010.023073
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.9886043
X-RAY DIFFRACTIONr_angle_other_deg0.937488
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.555519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95823.744203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.93915771
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9971526
X-RAY DIFFRACTIONr_chiral_restr0.0860.2676
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214759
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02923
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: 2.4→2.462 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.271 2445

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