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- PDB-7e3t: Crystal structure of TrmL from Mycoplasma capricolum -

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Basic information

Entry
Database: PDB / ID: 7e3t
TitleCrystal structure of TrmL from Mycoplasma capricolum
ComponentsPutative tRNA (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 (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
Putative tRNA (cytidine(34)-2'-O)-methyltransferase
Similarity search - Component
Biological speciesMycoplasma capricolum subsp. capricolum (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 Mycoplasma capricolum
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,2131
Polymers22,2131
Non-polymers00
Water57632
1
A: Putative tRNA (cytidine(34)-2'-O)-methyltransferase

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


Theoretical massNumber of molelcules
Total (without water)44,4272
Polymers44,4272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
Buried area4080 Å2
ΔGint-20 kcal/mol
Surface area15780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.824, 79.824, 117.333
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

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


Mass: 22213.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma capricolum subsp. capricolum (bacteria)
Gene: trmL-1, trmL-2, MCGM508_00050, MCGM508_04410 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0C2ZKK6, tRNA (cytidine34-2'-O)-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES monohydrate pH 6.5, 0.05M Cesium chloride, 30%v/v Jeffamine M-600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 13552 / % possible obs: 99.9 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.031 / Rrim(I) all: 0.101 / Χ2: 0.668 / Net I/σ(I): 3.9 / Num. measured all: 137705
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.148.61.3886520.7140.4821.4740.48299.8
2.14-2.189.21.2136590.7060.4051.2830.485100
2.18-2.2291.0016590.770.3391.060.462100
2.22-2.2610.60.9526480.8570.29310.482100
2.26-2.31110.8326540.8840.2480.8710.522100
2.31-2.3710.90.7656730.8860.230.8010.529100
2.37-2.4210.90.5636630.9470.170.590.568100
2.42-2.4910.80.4866710.9420.1490.5110.566100
2.49-2.5610.50.4056470.9540.1250.4250.57399.8
2.56-2.6510.30.3416710.9610.1080.3590.579100
2.65-2.749.70.2756640.9750.090.290.557100
2.74-2.8510.80.2356770.980.0720.2470.645100
2.85-2.9810.80.1886710.9840.0590.1980.67699.9
2.98-3.1410.70.1476770.9890.0470.1550.742100
3.14-3.3310.30.1146780.9910.0370.120.84499.9
3.33-3.599.50.0886840.9940.030.0940.897100
3.59-3.9510.80.0726930.9950.0230.0760.99499.7
3.95-4.5210.30.0656970.9970.0220.0691.083100
4.52-5.79.40.0617220.9970.0210.0640.98499.7
5.7-509.10.0397920.9990.0140.0420.59699.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-20000.7.4data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KDZ

4kdz


Resolution: 2.1→44.77 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.258 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 708 5.2 %RANDOM
Rwork0.1947 ---
obs0.1971 12811 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120.4 Å2 / Biso mean: 47.885 Å2 / Biso min: 31.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å2-0.26 Å2-0 Å2
2---0.52 Å20 Å2
3---1.67 Å2
Refinement stepCycle: final / Resolution: 2.1→44.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1369 0 0 33 1402
Biso mean---50.83 -
Num. residues----174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131400
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171291
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.6381905
X-RAY DIFFRACTIONr_angle_other_deg1.3361.5792941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3225173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82422.08372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71315222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.941158
X-RAY DIFFRACTIONr_chiral_restr0.0680.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021602
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02346
LS refinement shellResolution: 2.1→2.151 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.243 50 -
Rwork0.243 882 -
obs--95.88 %

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