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- PDB-7e3r: Crystal structure of TrmL from Vibrio vulnificus -

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Basic information

Entry
Database: PDB / ID: 7e3r
TitleCrystal structure of TrmL from Vibrio vulnificus
ComponentstRNA (cytidine(34)-2'-O)-methyltransferase
KeywordsTRANSFERASE / tRNA modification / methyltransferase / SAM / SAH / tRNA_Leu / cytidine/uridine-2'-O-methyltransferase
Function / homology
Function and homology information


wobble position cytosine ribose methylation / wobble position uridine ribose methylation / tRNA (cytidine34-2'-O)-methyltransferase / tRNA methyltransferase activity / S-adenosylmethionine-dependent methyltransferase activity / RNA binding / identical protein binding / cytoplasm
Similarity search - Function
tRNA (cytidine/uridine-2'-O-)-methyltransferase / tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases
Similarity search - Domain/homology
tRNA (cytidine(34)-2'-O)-methyltransferase
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsKim, J. / Son, J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To be published
Title: Crystal structure of tRNA mehtyltransferase TrmL from Vibrio vulnificus
Authors: Kim, J. / Son, J.
History
DepositionFeb 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA (cytidine(34)-2'-O)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)18,8571
Polymers18,8571
Non-polymers00
Water1,06359
1
A: tRNA (cytidine(34)-2'-O)-methyltransferase

A: tRNA (cytidine(34)-2'-O)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)37,7132
Polymers37,7132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3150 Å2
ΔGint-15 kcal/mol
Surface area13230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.290, 52.290, 119.689
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein tRNA (cytidine(34)-2'-O)-methyltransferase / RNA_Leu (C/U34) methyltransferase / tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmL


Mass: 18856.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: MO6-24/O / Gene: trmL, CRN52_04235 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A1W6M7K7, tRNA (cytidine34-2'-O)-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.17 Å3/Da / Density % sol: 43.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1M Tris-hydrochloride pH 8.5, 8% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97957 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 16324 / % possible obs: 99.4 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.025 / Rrim(I) all: 0.084 / Χ2: 0.95 / Net I/σ(I): 7 / Num. measured all: 174716
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.817.50.8337490.940.2580.8750.44693.3
1.81-1.848.10.6997870.9650.2160.7340.43796.9
1.84-1.888.90.7277750.9910.2240.7630.47698.9
1.88-1.929.60.6037890.9780.1840.6320.54399.4
1.92-1.9610.20.5117970.990.1540.5350.493100
1.96-210.60.5118150.9940.1560.5350.487100
2-2.0511.10.4697900.9940.1420.4910.534100
2.05-2.1110.90.388130.9920.1170.3980.578100
2.11-2.1710.20.3328150.9940.1070.3490.532100
2.17-2.2410.60.277890.9930.0850.2840.708100
2.24-2.3210.80.2438100.9950.0760.2550.698100
2.32-2.4212.10.1798090.9970.0520.1870.726100
2.42-2.5312.10.168210.9960.0470.1670.762100
2.53-2.66120.1298070.9980.0380.1350.836100
2.66-2.8311.90.118290.9980.0320.1151.034100
2.83-3.0411.90.0868310.9990.0260.0891.267100
3.04-3.3511.80.078310.9990.0210.0741.578100
3.35-3.83110.0578520.9990.0180.062.05799.9
3.83-4.8310.30.0458650.9980.0150.0482.073100
4.83-5011.90.049500.9990.0120.0421.74999.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KDZ

4kdz


Resolution: 1.79→39.41 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.543 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2425 860 5.3 %RANDOM
Rwork0.2 ---
obs0.2023 15402 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.49 Å2 / Biso mean: 40.292 Å2 / Biso min: 28.16 Å2
Baniso -1Baniso -2Baniso -3
1-2.81 Å2-0 Å2-0 Å2
2--2.81 Å2-0 Å2
3----5.62 Å2
Refinement stepCycle: final / Resolution: 1.79→39.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1139 0 0 59 1198
Biso mean---45.63 -
Num. residues----146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131164
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171092
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.6451577
X-RAY DIFFRACTIONr_angle_other_deg1.3411.5712495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2945144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.09121.04567
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78815182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5221510
X-RAY DIFFRACTIONr_chiral_restr0.0790.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021341
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02287
LS refinement shellResolution: 1.79→1.833 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.383 55 -
Rwork0.383 943 -
obs--84.86 %

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