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- PDB-5i5n: Crystal Structure of N-terminal Domain of Matrix Protein of Thogo... -

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Basic information

Entry
Database: PDB / ID: 5i5n
TitleCrystal Structure of N-terminal Domain of Matrix Protein of Thogoto Virus at Acidic 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: 1.418 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 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water5,278293
1
B: Matrix protein


Theoretical massNumber of molelcules
Total (without water)17,2161
Polymers17,2161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 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)36.982, 88.353, 88.346
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.: 293 / 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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.1M Sodium acetate trihydrate pH 4.5, 3.0M NaCl

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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: Jul 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989 Å / Relative weight: 1
ReflectionResolution: 1.418→39.51 Å / Num. obs: 55605 / % possible obs: 99.68 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 26.7
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 4.65 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PHENIXphasing
PHENIXmodel building
HKL-3000data processing
HKL-3000data scaling
HKL-3000data reduction
HKL-3000data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.418→39.51 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1898 2003 3.6 %
Rwork0.176 --
obs0.1766 55605 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.418→39.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2138 0 0 293 2431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.022168
X-RAY DIFFRACTIONf_angle_d1.642922
X-RAY DIFFRACTIONf_dihedral_angle_d13.025824
X-RAY DIFFRACTIONf_chiral_restr0.096340
X-RAY DIFFRACTIONf_plane_restr0.007374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4177-1.45320.24161410.20473727X-RAY DIFFRACTION99
1.4532-1.49250.21121400.18033769X-RAY DIFFRACTION99
1.4925-1.53640.20651410.17083785X-RAY DIFFRACTION100
1.5364-1.5860.21351410.16693724X-RAY DIFFRACTION99
1.586-1.64270.19541420.16453806X-RAY DIFFRACTION100
1.6427-1.70850.19011410.16373804X-RAY DIFFRACTION100
1.7085-1.78620.22041420.16863807X-RAY DIFFRACTION100
1.7862-1.88040.191420.16823829X-RAY DIFFRACTION100
1.8804-1.99820.19681410.17273789X-RAY DIFFRACTION100
1.9982-2.15250.18631460.16933876X-RAY DIFFRACTION100
2.1525-2.36910.1921420.1763814X-RAY DIFFRACTION100
2.3691-2.71180.19131430.18123868X-RAY DIFFRACTION100
2.7118-3.41630.17341450.17913930X-RAY DIFFRACTION100
3.4163-39.52550.17971560.18034074X-RAY DIFFRACTION100

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