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- PDB-8bxk: Ntaya virus methyltransferase -

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Basic information

Entry
Database: PDB / ID: 8bxk
TitleNtaya virus methyltransferase
ComponentsNtaya virus methyltransferase
KeywordsTRANSFERASE / methyltransferase / NS5 / flavivirus
Function / homologySINEFUNGIN
Function and homology information
Biological speciesNtaya virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsBoura, E. / Krafcikova, P.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)LX22NPO5103European Union
CitationJournal: To Be Published
Title: Ntaya virus methyltransferase
Authors: Boura, E. / Krafcikova, P.
History
DepositionDec 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.accession_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ntaya virus methyltransferase
B: Ntaya virus methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0704
Polymers60,3072
Non-polymers7632
Water6,161342
1
A: Ntaya virus methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5352
Polymers30,1541
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ntaya virus methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5352
Polymers30,1541
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.090, 110.060, 116.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Ntaya virus methyltransferase


Mass: 30153.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ntaya virus / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.92 Å3/Da / Density % sol: 57.89 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 4.0 M Sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Nov 8, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.31→39.96 Å / Num. obs: 27743 / % possible obs: 87.16 % / Redundancy: 6.3 % / Biso Wilson estimate: 24.36 Å2 / CC1/2: 0.998 / CC star: 1 / Net I/σ(I): 16.4
Reflection shellResolution: 2.31→2.39 Å / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1077 / CC1/2: 0.966

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MRK

5mrk


Resolution: 2.31→39.96 Å / SU ML: 0.242 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.8576
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2348 1393 5.03 %
Rwork0.2008 26315 -
obs0.2025 27708 86.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.56 Å2
Refinement stepCycle: LAST / Resolution: 2.31→39.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4144 0 54 342 4540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00274286
X-RAY DIFFRACTIONf_angle_d0.48925778
X-RAY DIFFRACTIONf_chiral_restr0.0395607
X-RAY DIFFRACTIONf_plane_restr0.0031745
X-RAY DIFFRACTIONf_dihedral_angle_d15.70191616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.390.2421520.2068966X-RAY DIFFRACTION32.25
2.39-2.480.2696970.22411741X-RAY DIFFRACTION59.12
2.48-2.60.29461080.24532409X-RAY DIFFRACTION79.73
2.6-2.730.27441510.24752911X-RAY DIFFRACTION97.14
2.73-2.90.28981480.23893027X-RAY DIFFRACTION99.91
2.9-3.130.29721550.23672994X-RAY DIFFRACTION99.94
3.13-3.440.26451770.21763015X-RAY DIFFRACTION99.72
3.44-3.940.20221610.17133019X-RAY DIFFRACTION99.16
3.94-4.960.18391760.15653026X-RAY DIFFRACTION98.8
4.96-39.960.20521680.18473207X-RAY DIFFRACTION99.47

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