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- PDB-8k1f: Crystal Structure of TrmR from Fusobacterium nucleatum -

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Basic information

Entry
Database: PDB / ID: 8k1f
TitleCrystal Structure of TrmR from Fusobacterium nucleatum
ComponentstRNA 5-hydroxyuridine methyltransferase
KeywordsTRANSFERASE / tRNA 5-hydroxyuridine methyltransferase
Function / homology
Function and homology information


tRNA (uridine) methyltransferase activity / tRNA methylation / O-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / magnesium ion binding
Similarity search - Function
tRNA 5-hydroxyuridine methyltransferase / : / Class I-like SAM-dependent O-methyltransferase / O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
tRNA 5-hydroxyuridine methyltransferase
Similarity search - Component
Biological speciesFusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsHe, S.R. / Bai, X. / Zhang, J. / Zhao, Z.D.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal Structure of TrmR from Fusobacterium nucleatum
Authors: He, S.R. / Bai, X.
History
DepositionJul 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA 5-hydroxyuridine methyltransferase
B: tRNA 5-hydroxyuridine methyltransferase
C: tRNA 5-hydroxyuridine methyltransferase


Theoretical massNumber of molelcules
Total (without water)75,2063
Polymers75,2063
Non-polymers00
Water00
1
A: tRNA 5-hydroxyuridine methyltransferase

C: tRNA 5-hydroxyuridine methyltransferase


Theoretical massNumber of molelcules
Total (without water)50,1372
Polymers50,1372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area2670 Å2
ΔGint-20 kcal/mol
Surface area16640 Å2
MethodPISA
2
B: tRNA 5-hydroxyuridine methyltransferase

B: tRNA 5-hydroxyuridine methyltransferase


Theoretical massNumber of molelcules
Total (without water)50,1372
Polymers50,1372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3310 Å2
ΔGint-30 kcal/mol
Surface area16340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.281, 46.589, 87.316
Angle α, β, γ (deg.)90.00, 98.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein tRNA 5-hydroxyuridine methyltransferase / ho5U methyltransferase


Mass: 25068.719 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)
Gene: trmR, FN0314 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: Q8RGI1, Transferases; Transferring one-carbon groups; Methyltransferases

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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: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M MES, 9% PEG 8000, 95mM calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→36.1 Å / Num. obs: 110870 / % possible obs: 80.79 % / Redundancy: 4.6 % / Biso Wilson estimate: 32.33 Å2 / Rsym value: 0.053 / Net I/σ(I): 11.2
Reflection shellResolution: 2.4→2.486 Å / Num. unique obs: 23951 / Rsym value: 0.053

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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: 2.4→36.097 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 31.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2923 2000 9.45 %
Rwork0.2131 --
obs0.2206 21154 80.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→36.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4374 0 0 0 4374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094432
X-RAY DIFFRACTIONf_angle_d0.9475993
X-RAY DIFFRACTIONf_dihedral_angle_d3.3672622
X-RAY DIFFRACTIONf_chiral_restr0.054702
X-RAY DIFFRACTIONf_plane_restr0.005764
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4004-2.46040.4127480.2485461X-RAY DIFFRACTION27
2.4604-2.52690.3601630.2454610X-RAY DIFFRACTION37
2.5269-2.60120.3203860.2565808X-RAY DIFFRACTION48
2.6012-2.68520.29931090.26121058X-RAY DIFFRACTION64
2.6852-2.78110.33121370.26151304X-RAY DIFFRACTION77
2.7811-2.89240.3371610.27061550X-RAY DIFFRACTION92
2.8924-3.0240.33111680.26381606X-RAY DIFFRACTION96
3.024-3.18330.35821730.2431654X-RAY DIFFRACTION97
3.1833-3.38260.31751700.22111624X-RAY DIFFRACTION97
3.3826-3.64360.29021740.19791676X-RAY DIFFRACTION99
3.6436-4.00980.25671740.18451663X-RAY DIFFRACTION99
4.0098-4.58910.22451770.16611688X-RAY DIFFRACTION99
4.5891-5.77790.27171780.18821706X-RAY DIFFRACTION99
5.7779-36.0970.2931820.21751746X-RAY DIFFRACTION99

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