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- PDB-8b1n: Crystal structure of TrmD-Tm1570 from Calditerrivibrio nitroreduc... -

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Basic information

Entry
Database: PDB / ID: 8b1n
TitleCrystal structure of TrmD-Tm1570 from Calditerrivibrio nitroreducens in complex with S-adenosyl-L-methionine
ComponentstRNA (guanine-N(1)-)-methyltransferase
KeywordsTRANSFERASE / TrmD-Tm1570 / TrmD / Tm1570 / Methyl Transferase / Knotted Protein / Double 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 / 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: 2 Å
AuthorsKluza, A. / Lewandowska, I. / Augustyniak, R. / 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: Front Mol Biosci / Year: 2023
Title: Are there double knots in proteins? Prediction and in vitro verification based on TrmD-Tm1570 fusion from C. nitroreducens.
Authors: Perlinska, A.P. / Nguyen, M.L. / Pilla, S.P. / Staszor, E. / Lewandowska, I. / Bernat, A. / Purta, E. / Augustyniak, R. / Bujnicki, J.M. / Sulkowska, J.I.
History
DepositionSep 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)102,51520
Polymers99,9942
Non-polymers2,52118
Water11,980665
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14700 Å2
ΔGint-107 kcal/mol
Surface area33840 Å2
Unit cell
Length a, b, c (Å)96.780, 199.560, 56.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-985-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 49997.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Calditerrivibrio nitroreducens DSM 19672 (bacteria)
Strain: DSM 19672 / NBRC 101217 / Yu37-1 / Gene: trmD, Calni_2012 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: E4THH1, tRNA (guanine37-N1)-methyltransferase

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Non-polymers , 5 types, 683 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 665 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.74 Å3/Da / Density % sol: 55.07 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: Protein sample: 5.7 mg/mL TrmD-Tm1570 in 50 mM HEPES buffer pH 7.4, 300 mM NaCl, 5% glycerol, with addition of 3 mM SAM, 0.1% DDM and 3000x diluted seeds stock. Reservoir solution: 0.2 M ...Details: Protein sample: 5.7 mg/mL TrmD-Tm1570 in 50 mM HEPES buffer pH 7.4, 300 mM NaCl, 5% glycerol, with addition of 3 mM SAM, 0.1% DDM and 3000x diluted seeds stock. Reservoir solution: 0.2 M MgCl2, 0.1 M Tris pH 7.0, 10% PEG 8000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→49.3 Å / Num. obs: 75191 / % possible obs: 99.9 % / Redundancy: 8.81 % / Biso Wilson estimate: 33.68 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.138 / Net I/σ(I): 13.68
Reflection shellResolution: 2→2.12 Å / Redundancy: 8.69 % / Mean I/σ(I) obs: 1.43 / Num. unique obs: 11921 / CC1/2: 0.616 / Rrim(I) all: 1.523 / % possible all: 99.4

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIXmodel building
Cootmodel building
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WYR, 3DCM

5wyr

3dcm


Resolution: 2→48.92 Å / SU ML: 0.2285 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.6871
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2088 2100 2.79 %
Rwork0.1691 73068 -
obs0.1703 75168 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.87 Å2
Refinement stepCycle: LAST / Resolution: 2→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6679 0 162 665 7506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00657119
X-RAY DIFFRACTIONf_angle_d0.82419661
X-RAY DIFFRACTIONf_chiral_restr0.05311083
X-RAY DIFFRACTIONf_plane_restr0.00431224
X-RAY DIFFRACTIONf_dihedral_angle_d17.22082675
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.33571370.29014742X-RAY DIFFRACTION98.51
2.05-2.10.29271380.2644815X-RAY DIFFRACTION99.96
2.1-2.150.25971380.23794798X-RAY DIFFRACTION99.98
2.15-2.220.26521380.21474802X-RAY DIFFRACTION99.94
2.22-2.290.25011390.21234846X-RAY DIFFRACTION100
2.29-2.370.24221390.19714820X-RAY DIFFRACTION100
2.37-2.470.23861390.18444842X-RAY DIFFRACTION99.98
2.47-2.580.2181390.17284840X-RAY DIFFRACTION99.98
2.58-2.710.21551380.1744847X-RAY DIFFRACTION99.98
2.71-2.880.22811400.17844864X-RAY DIFFRACTION99.98
2.88-3.110.21281400.17284885X-RAY DIFFRACTION100
3.11-3.420.20911400.16114876X-RAY DIFFRACTION100
3.42-3.910.17891420.14524934X-RAY DIFFRACTION100
3.91-4.930.15091430.12344975X-RAY DIFFRACTION99.98
4.93-48.920.21371500.16875182X-RAY DIFFRACTION99.44
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)
11.65162000129-0.299648270363-0.06764833293862.325848035290.4683699070141.25761456601-0.0313803689924-0.07604402572280.1299567866520.205896481721-0.0167600821140.433541604622-0.0571818398736-0.1691362017160.04705313503320.1837572917450.01749858288730.04924074499080.2166103257620.01172680523680.30478130804959.503028868479.088511074180.1761740606
23.48035048187-0.1425569072110.3205709474764.746870939580.2651600041011.899612152030.08174346348070.144694378620.183361056259-0.0710590399522-0.0420733440008-0.306396374576-0.2028879553670.140031372226-0.0388038535730.2465796507280.001616840001640.02346553179260.2566231260870.04326805666620.183290610277116.04913055864.992725886383.4999269613
31.94535776479-0.292211091077-0.0507718751532.687070762870.5358472861831.593857639040.03830477280170.3412519305330.0530016649706-0.465244156784-0.03653853422290.223920029372-0.111864674198-0.123850784369-0.005104099396030.2668278501660.0243928223267-0.03438400269580.2968628558680.04102779294450.198676528368.49428790772.144090144557.7819602735
43.40065521065-0.292862903764-1.180696659075.38313194211.328488268322.611038708760.0589910909775-0.1483058785510.4057401815890.1233562092660.11849081151-0.439807542808-0.279129227990.231410533193-0.1602263382660.300625067371-0.0266907495555-0.02594030452310.238439189098-0.03955373072120.38032480017476.423790558596.487875613982.4843591968
52.874535549210.07104086023830.2712008580252.10652734903-0.7359509435852.87898320529-0.0611799547592-0.3539980339070.04875056793190.23568447208-2.60721211447E-50.059063977007-0.222792477487-0.2408807435570.06504712898180.3137455595640.07868947461110.05791630884670.309414738706-0.008136321284290.20823833116596.737282819165.297098959799.9222200889
63.131012075610.3795711282651.7728216442.573317151251.021182919654.605469537650.06318678458460.0677660816784-0.3545194756740.0831213346141-6.23792479523E-5-0.006312619067240.3407512753590.156400384238-0.06402862932720.238418799940.06529435408090.02477268428190.2399294646050.02526154121830.23270757292384.644962877856.665707919567.8975300017
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 159 )
2X-RAY DIFFRACTION2chain 'A' and (resid 248 through 430 )
3X-RAY DIFFRACTION3chain 'B' and (resid 0 through 159 )
4X-RAY DIFFRACTION4chain 'B' and (resid 160 through 241 )
5X-RAY DIFFRACTION5chain 'B' and (resid 247 through 429 )
6X-RAY DIFFRACTION6chain 'A' and (resid 160 through 247)

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