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- PDB-8k5l: Structure of tRNA (cmo5U34)-methyltransferase from Fusobacterium ... -

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Basic information

Entry
Database: PDB / ID: 8k5l
TitleStructure of tRNA (cmo5U34)-methyltransferase from Fusobacterium nucleatum
ComponentstRNA (cmo5U34)-methyltransferase
KeywordsTRANSFERASE / tRNA (cmo5U34)-methyltransferase
Function / homologyVaccinia Virus protein VP39 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesFusobacterium nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.67 Å
AuthorsHe, S.R. / Bai, X.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal Structure of CmoA from Fusobacterium nucleatum
Authors: He, S.R. / Bai, X.
History
DepositionJul 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA (cmo5U34)-methyltransferase
B: tRNA (cmo5U34)-methyltransferase
C: tRNA (cmo5U34)-methyltransferase
D: tRNA (cmo5U34)-methyltransferase
E: tRNA (cmo5U34)-methyltransferase
F: tRNA (cmo5U34)-methyltransferase
G: tRNA (cmo5U34)-methyltransferase
H: tRNA (cmo5U34)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)198,0378
Polymers198,0378
Non-polymers00
Water4,468248
1
A: tRNA (cmo5U34)-methyltransferase
B: tRNA (cmo5U34)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)49,5092
Polymers49,5092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-8 kcal/mol
Surface area17830 Å2
MethodPISA
2
C: tRNA (cmo5U34)-methyltransferase
D: tRNA (cmo5U34)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)49,5092
Polymers49,5092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-8 kcal/mol
Surface area17660 Å2
MethodPISA
3
E: tRNA (cmo5U34)-methyltransferase
F: tRNA (cmo5U34)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)49,5092
Polymers49,5092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-8 kcal/mol
Surface area18110 Å2
MethodPISA
4
G: tRNA (cmo5U34)-methyltransferase
H: tRNA (cmo5U34)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)49,5092
Polymers49,5092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-9 kcal/mol
Surface area18000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.955, 58.980, 139.690
Angle α, β, γ (deg.)90.03, 90.03, 90.05
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
tRNA (cmo5U34)-methyltransferase


Mass: 24754.656 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum (bacteria) / Production host: Escherichia coli K-12 (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 28% peg 2000, 200mM ammonia sulfate, 0.1M Sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.67→31.07 Å / Num. obs: 204553 / % possible obs: 93.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 27 Å2 / CC1/2: 0.995 / Net I/σ(I): 1.38
Reflection shellResolution: 1.67→1.71 Å / Num. unique obs: 10475 / Rrim(I) all: 0.058

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.67→31.067 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 27.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2567 10162 4.97 %
Rwork0.2249 --
obs0.2265 204392 93.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.67→31.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12860 0 0 248 13108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713102
X-RAY DIFFRACTIONf_angle_d0.79717642
X-RAY DIFFRACTIONf_dihedral_angle_d2.9868082
X-RAY DIFFRACTIONf_chiral_restr0.0532042
X-RAY DIFFRACTIONf_plane_restr0.0042202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6702-1.68920.33542180.32324141X-RAY DIFFRACTION60
1.6892-1.70910.34562540.31664491X-RAY DIFFRACTION66
1.7091-1.72990.36252640.30465448X-RAY DIFFRACTION77
1.7299-1.75180.30392980.30256112X-RAY DIFFRACTION90
1.7518-1.77490.3323780.28786497X-RAY DIFFRACTION92
1.7749-1.79920.31164060.27546288X-RAY DIFFRACTION94
1.7992-1.82490.30612720.26726661X-RAY DIFFRACTION95
1.8249-1.85210.29734350.26246660X-RAY DIFFRACTION96
1.8521-1.88110.29923500.2776628X-RAY DIFFRACTION96
1.8811-1.91190.29954050.27986583X-RAY DIFFRACTION96
1.9119-1.94490.3183420.28036718X-RAY DIFFRACTION96
1.9449-1.98020.31383970.26876580X-RAY DIFFRACTION97
1.9802-2.01830.29023700.26696645X-RAY DIFFRACTION97
2.0183-2.05950.3213060.26746732X-RAY DIFFRACTION97
2.0595-2.10430.31833190.25596826X-RAY DIFFRACTION97
2.1043-2.15320.24873730.2436613X-RAY DIFFRACTION97
2.1532-2.2070.35363540.25486781X-RAY DIFFRACTION97
2.207-2.26670.29553230.24746753X-RAY DIFFRACTION97
2.2667-2.33340.27482910.23716759X-RAY DIFFRACTION97
2.3334-2.40870.26373590.23986651X-RAY DIFFRACTION97
2.4087-2.49470.24233510.24266791X-RAY DIFFRACTION97
2.4947-2.59450.30533630.23836697X-RAY DIFFRACTION97
2.5945-2.71260.25194400.24146642X-RAY DIFFRACTION97
2.7126-2.85550.29213520.23256755X-RAY DIFFRACTION97
2.8555-3.03420.25923840.24046713X-RAY DIFFRACTION98
3.0342-3.26830.2442480.23636945X-RAY DIFFRACTION98
3.2683-3.59670.2813260.22716815X-RAY DIFFRACTION98
3.5967-4.11620.20713410.18296804X-RAY DIFFRACTION98
4.1162-5.18210.17373760.16286762X-RAY DIFFRACTION98
5.1821-31.0670.23582670.18826739X-RAY DIFFRACTION96

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