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- PDB-7e3s: Crystal structure of TrmL from Shewanella oneidensis -

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Basic information

Entry
Database: PDB / ID: 7e3s
TitleCrystal structure of TrmL from Shewanella oneidensis
ComponentstRNA (cytidine(34)-2'-O)-methyltransferase
KeywordsTRANSFERASE / tRNA modification / methyltransferase / SAM / SAH / tRNA_Leu / cytidine/uridine(34)-2'-O-methyltransferase
Function / homology
Function and homology information


: / wobble position cytosine ribose methylation / wobble position uridine ribose methylation / tRNA (cytidine(34)-2'-O)-methyltransferase activity / tRNA (5-carboxymethylaminomethyluridine(34)-2'-O)-methyltransferase activity / tRNA (cytidine34-2'-O)-methyltransferase / RNA 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 speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 TrmL from Shewanella oneidensis
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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,7752
Polymers40,7752
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-12 kcal/mol
Surface area12500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.816, 77.988, 101.044
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 0 - 154 / Label seq-ID: 30 - 184

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 20387.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (strain MR-1) (bacteria)
Strain: MR-1 / Gene: trmL, SO_4529 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8E8X2, tRNA (cytidine34-2'-O)-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 1.81 Å3/Da / Density % sol: 31.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M Ammonium acetate, 0.1M Sodium citrate tribasic dehydrate pH5.6, 30%w/v PEG 4000

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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: 2.09→50 Å / Num. obs: 17438 / % possible obs: 98.2 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.048 / Rrim(I) all: 0.161 / Χ2: 1.003 / Net I/σ(I): 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.146.11.0867520.7760.4271.1740.53285.6
2.14-2.186.20.9797740.8890.381.0570.53988.9
2.18-2.226.81.048170.8780.3921.1170.51994.2
2.22-2.267.40.8338600.9270.3060.8910.6197.2
2.26-2.318.40.9858660.9060.3471.0470.59498.7
2.31-2.379.60.7998690.9150.2650.8430.6100
2.37-2.4211.10.8138690.9620.2520.8520.56100
2.42-2.4911.60.7648730.9680.2320.7990.604100
2.49-2.56120.6538930.9730.1950.6820.648100
2.56-2.6512.10.5718570.9770.170.5970.649100
2.65-2.7412.20.4468880.9840.1320.4650.689100
2.74-2.8512.20.4118930.9910.1220.4290.721100
2.85-2.9812.30.2988660.990.0880.3110.787100
2.98-3.1412.30.2318990.9940.0690.2410.934100
3.14-3.3312.20.1818800.9940.0540.1890.966100
3.33-3.5911.70.138990.9960.0390.1361.122100
3.59-3.9510.80.1038910.9970.0330.1091.441100
3.95-4.5210.60.088980.9950.0260.0841.74299.8
4.52-5.713.70.0739230.9970.0210.0761.893100
5.7-50130.0689710.9990.020.0712.33899.8

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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: 2.1→39.02 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.141 / SU ML: 0.191 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2389 859 4.9 %RANDOM
Rwork0.1861 ---
obs0.1886 16558 96.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.64 Å2 / Biso mean: 41.094 Å2 / Biso min: 27.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20 Å2-0 Å2
2--4.1 Å2-0 Å2
3----5.24 Å2
Refinement stepCycle: final / Resolution: 2.1→39.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2256 0 0 85 2341
Biso mean---46.65 -
Num. residues----300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132302
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172183
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.6383124
X-RAY DIFFRACTIONr_angle_other_deg1.2641.5695001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.365297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.68221.869107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52415367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4151514
X-RAY DIFFRACTIONr_chiral_restr0.0670.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022621
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02523
Refine LS restraints NCS

Ens-ID: 1 / Number: 4066 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.14 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.425 42 -
Rwork0.33 854 -
obs--69.51 %

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