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- PDB-8ri0: Crystal structure of Tm1570 domain from Calditerrivibrio nitrored... -

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Basic information

Entry
Database: PDB / ID: 8ri0
TitleCrystal structure of Tm1570 domain from Calditerrivibrio nitroreducens in complex with S-adenosyl-L-methionine
ComponentstRNA (guanine-N(1)-)-methyltransferase
KeywordsTRANSFERASE / TrmD-Tm1570 / Tm1570 / Knotted Protein
Function / homology
Function and homology information


tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA N1-guanine methylation / metal ion binding / cytosol
Similarity search - Function
tRNA (guanine-N(1)-)-methyltransferase, C-terminal / SAM-dependent RNA methyltransferase / tRNA (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase TrmD / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesCalditerrivibrio nitroreducens DSM 19672 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKluza, A. / Lewandowska, I. / Sulkowska, J.
Funding support Poland, European Union, 2items
OrganizationGrant numberCountry
Polish National Science Centre2018/31/B/NZ1/04016 Poland
European Union (EU)COST EUTOPIA actionEuropean Union
CitationJournal: To Be Published
Title: Are there double knots in proteins? Prediction and in vitro verification based on TrmD-Tm1570 fusion from C. nitroreducens. To be published
Authors: Sulkowska, J.
History
DepositionDec 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA (guanine-N(1)-)-methyltransferase
B: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7354
Polymers46,9382
Non-polymers7972
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-8 kcal/mol
Surface area14790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.850, 48.090, 79.810
Angle α, β, γ (deg.)90.000, 116.220, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-636-

HOH

21A-649-

HOH

31B-654-

HOH

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Components

#1: Protein tRNA (guanine-N(1)-)-methyltransferase / M1G-methyltransferase / tRNA [GM37] methyltransferase


Mass: 23468.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Calditerrivibrio nitroreducens DSM 19672 (bacteria)
Gene: trmD, Calni_2012 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: E4THH1, tRNA (guanine37-N1)-methyltransferase
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 1.94 Å3/Da / Density % sol: 36.77 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: Protein solution: 20 mg/mL Tm1570 in 50 mM HEPES buffer pH 7.4, 300 mM NaCl, 5% glycerol, with addition of 5 mM SAM, 5 mM MgCl2, 0.1% DDM. Reservoir solution: 0.1 M Tris pH 8.5, 20% v/v ethanol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.95→47.48 Å / Num. obs: 26147 / % possible obs: 98.4 % / Redundancy: 3.31 % / Biso Wilson estimate: 36.82 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.073 / Net I/σ(I): 10.04
Reflection shellResolution: 1.95→2.07 Å / Redundancy: 3.44 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4233 / CC1/2: 0.696 / Rrim(I) all: 0.959 / % possible all: 99.4

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIX1.17.1_3660refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→30.66 Å / SU ML: 0.2781 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.3311
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.25 1999 7.65 %
Rwork0.206 24123 -
obs0.2093 26122 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.99 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2545 0 54 103 2702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00682677
X-RAY DIFFRACTIONf_angle_d0.94533656
X-RAY DIFFRACTIONf_chiral_restr0.0599440
X-RAY DIFFRACTIONf_plane_restr0.0055460
X-RAY DIFFRACTIONf_dihedral_angle_d17.927945
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.44391440.37631731X-RAY DIFFRACTION99.31
2-2.050.3881400.34131700X-RAY DIFFRACTION99.3
2.05-2.110.38111440.31631722X-RAY DIFFRACTION98.52
2.11-2.180.31351420.28691723X-RAY DIFFRACTION99.31
2.18-2.260.28831410.24971707X-RAY DIFFRACTION98.88
2.26-2.350.28891430.24091718X-RAY DIFFRACTION98
2.35-2.460.27051420.23121712X-RAY DIFFRACTION99.52
2.46-2.590.2741450.21991752X-RAY DIFFRACTION98.85
2.59-2.750.23611420.21071708X-RAY DIFFRACTION99.09
2.75-2.960.27391430.21321723X-RAY DIFFRACTION98.47
2.96-3.260.25551420.20711716X-RAY DIFFRACTION98.05
3.26-3.730.26151440.18821743X-RAY DIFFRACTION98.59
3.73-4.690.20861390.16181682X-RAY DIFFRACTION95.29
4.69-30.660.2011480.18311786X-RAY DIFFRACTION97.87
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.25775805376-0.3712697184062.010811880453.235711902461.814641746177.120328888560.0545074756829-0.4161468361240.3275221938880.209789061711-0.1162136894130.132218566637-0.340227245602-0.550684058230.06561143878730.492661765316-0.0006048411499970.06600752655440.407184799732-0.1164440561690.3560017446950.2112759434070.19548294647227.7893731955
22.38906079528-0.1526254644861.016107098362.848805122340.09962061990262.19107856309-0.0970334411454-0.544327147345-0.06857428098430.1428517543780.07268042796780.3685194309650.0744759084462-0.4993844327880.05231324239040.624725762049-0.007370393630690.137107529510.6074006735-0.06541072763350.406983865427-5.46926373251-5.8977296866329.3645888844
37.219124339590.345801263088-1.178953633326.18121313216-0.6773244635364.25538619855-0.0537313988104-0.383748834615-0.263726735920.0640383253252-0.165266214851-0.1624440982010.7344097965730.2486767192480.1456272385590.480412682026-0.02696433088380.06166175926630.332605617127-0.0006216624346660.2672643582074.78452831452-12.978695875723.4661266183
43.362064327010.206596579612-1.072354291917.04470524433-3.110197227286.674688481490.0942399903867-0.2095545097780.3325018011890.474142496245-0.0938289956066-0.16540649862-0.3812242926240.1504897366860.01317941690760.248387759088-0.00462993119610.02323701874330.31731144117-0.005270162981770.37462768608319.1829621056-0.36939190643912.5079187623
53.957366357320.5505277395630.9543617532723.253569971360.7354072709353.038467752810.1439796819480.4044792127540.0730201294612-0.0978284008434-0.00930743749195-0.2578900047920.1444641026170.246743244123-0.1094932402650.3566038664910.0652487425080.06956513161570.3149556542160.0405110105310.34329847804720.94270395-5.680196266237.38558194859
64.63122676448-0.961642344351-1.283598861061.758739433971.561748995515.78531005972-0.07902075336930.0337488254907-0.0344876362813-0.264480203880.02282484809520.1212755454550.370577150908-0.3073869572740.05354126487280.38164812472-0.00404557767801-0.009665644391340.2496572452180.001498069393320.2601883068697.90027447976-9.209079111579.88815150344
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 247 through 296)
2X-RAY DIFFRACTION2chain 'A' and (resid 297 through 394 )
3X-RAY DIFFRACTION3chain 'A' and (resid 395 through 430 )
4X-RAY DIFFRACTION4chain 'B' and (resid 247 through 296)
5X-RAY DIFFRACTION5chain 'B' and (resid 297 through 394 )
6X-RAY DIFFRACTION6chain 'B' and (resid 395 through 430 )

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