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- PDB-7e3q: Crystal structure of SAH bound TrmL from Vibrio vulnificus -

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Basic information

Entry
Database: PDB / ID: 7e3q
TitleCrystal structure of SAH bound 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
S-ADENOSYL-L-HOMOCYSTEINE / tRNA (cytidine(34)-2'-O)-methyltransferase
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 SAH bound 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 ...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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0413
Polymers37,6572
Non-polymers3841
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-16 kcal/mol
Surface area14110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.354, 67.354, 145.611
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 1 - 158 / Label seq-ID: 1 - 158

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

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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: 18828.512 Da / Num. of mol.: 2
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: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-hydrochloride pH 8.5, 0.2M Magnesium chloride hexahydrate, 30% w/v PEG 4000, 40% v/v tert-Butano

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 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: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 9778 / % possible obs: 99.6 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.081 / Rrim(I) all: 0.22 / Χ2: 0.72 / Net I/σ(I): 2.9 / Num. measured all: 67737
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.7570.8214630.750.3280.8850.54199.8
2.75-2.87.20.8194910.8180.3220.8820.509100
2.8-2.857.20.6914580.8170.2720.7440.561100
2.85-2.917.20.6164820.9010.2410.6620.546100
2.91-2.9770.5834710.8510.2310.6280.58100
2.97-3.0470.5234790.8960.210.5640.626100
3.04-3.126.50.434690.8790.180.4680.63998.9
3.12-3.26.80.3754820.9280.1510.4060.583100
3.2-3.37.40.3474830.950.1330.3720.717100
3.3-3.47.20.2874890.9690.1110.3080.734100
3.4-3.527.30.2434810.9740.0940.2610.72399.8
3.52-3.667.10.2184830.9730.0860.2350.795100
3.66-3.837.10.1884810.9780.0740.2020.828100
3.83-4.036.70.1744910.9850.0710.1890.868100
4.03-4.296.70.1414850.9860.0580.1530.86798
4.29-4.627.20.1184900.9930.0460.1270.936100
4.62-5.0870.1185040.990.0470.1270.975100
5.08-5.816.60.1225130.990.050.1330.796100
5.81-7.326.40.1195210.990.0490.1290.73799.2
7.32-5060.0695620.9950.0290.0750.82196.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KDZ

4kdz


Resolution: 2.7→49.49 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.915 / SU B: 14.322 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.36 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2515 486 5 %RANDOM
Rwork0.1889 ---
obs0.1921 9254 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.47 Å2 / Biso mean: 34.985 Å2 / Biso min: 2.65 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å20 Å20 Å2
2--1.57 Å20 Å2
3----3.14 Å2
Refinement stepCycle: final / Resolution: 2.7→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2441 0 26 37 2504
Biso mean--34.27 25.11 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132533
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172311
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.6453441
X-RAY DIFFRACTIONr_angle_other_deg1.2711.575320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5785318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.19921.119134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.89115394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9221520
X-RAY DIFFRACTIONr_chiral_restr0.0680.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022885
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02554
Refine LS restraints NCS

Ens-ID: 1 / Number: 4399 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.701→2.771 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 33 -
Rwork0.303 654 -
all-687 -
obs--99.85 %

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