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- PDB-5i5o: Crystal Structure of N-terminal Domain of Matrix Protein of Thogo... -

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Basic information

Entry
Database: PDB / ID: 5i5o
TitleCrystal Structure of N-terminal Domain of Matrix Protein of Thogoto Virus at Neutral pH.
ComponentsMatrix protein
KeywordsVIRAL PROTEIN
Function / homologyMatrix/matrix long, N-terminal / Matrix and Matrix long proteins N-terminal / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / structural constituent of virion / Protein ML / Matrix protein
Function and homology information
Biological speciesThogoto virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.682 Å
AuthorsLiu, Y. / Liang, H. / Yang, M.
CitationJournal: J.Gen.Virol. / Year: 2016
Title: pH-dependent conformational changes of a Thogoto virus matrix protein reveal mechanisms of viral assembly and uncoating
Authors: Yang, M. / Feng, F. / Liu, Y. / Wang, H. / Yang, Z. / Hou, W. / Liang, H.
History
DepositionFeb 15, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrix protein
B: Matrix protein


Theoretical massNumber of molelcules
Total (without water)34,4312
Polymers34,4312
Non-polymers00
Water25214
1
A: Matrix protein


Theoretical massNumber of molelcules
Total (without water)17,2161
Polymers17,2161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Matrix protein


Theoretical massNumber of molelcules
Total (without water)17,2161
Polymers17,2161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.037, 73.298, 94.215
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Matrix protein


Mass: 17215.727 Da / Num. of mol.: 2 / Fragment: UNP residues 3-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thogoto virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q9E781, UniProt: Q80A33*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.86 Å3/Da / Density % sol: 33.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M Ammonium citrate tribasic pH 7.0, 20%(w/v) Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.989 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989 Å / Relative weight: 1
ReflectionResolution: 2.682→34.156 Å / Num. obs: 7381 / % possible obs: 97.5 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.1352 / Net I/σ(I): 12.93
Reflection shellResolution: 2.68→2.75 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 4.17 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
PHENIXphasing
PHENIXmodel building
HKL-3000data processing
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.682→34.156 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2852 737 9.99 %
Rwork0.2712 --
obs0.2726 7381 96.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.682→34.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2052 0 0 14 2066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112080
X-RAY DIFFRACTIONf_angle_d1.342800
X-RAY DIFFRACTIONf_dihedral_angle_d17.668790
X-RAY DIFFRACTIONf_chiral_restr0.051326
X-RAY DIFFRACTIONf_plane_restr0.005356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6817-2.88860.41341410.33331278X-RAY DIFFRACTION96
2.8886-3.17910.33311510.2941351X-RAY DIFFRACTION100
3.1791-3.63870.29651450.27831308X-RAY DIFFRACTION97
3.6387-4.58260.27711480.25921337X-RAY DIFFRACTION97
4.5826-34.15860.24951520.25741370X-RAY DIFFRACTION95

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