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- PDB-8byh: Crystal structure of TrmD domain from Calditerrivibrio nitroreduc... -

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Basic information

Entry
Database: PDB / ID: 8byh
TitleCrystal structure of TrmD domain from Calditerrivibrio nitroreducens in complex with S-adenosyl-L-methionine
ComponentstRNA (guanine-N(1)-)-methyltransferase
KeywordsTRANSFERASE / knotted-protein / tRNA / trmD / methyl transferase
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: 2.19 Å
AuthorsKluza, A. / Lewandowska, I. / Sulkowska, J.
Funding support Poland, European Union, 2items
OrganizationGrant numberCountry
Polish National Science CentreUMO-2018/31/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 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)57,06313
Polymers55,7582
Non-polymers1,30611
Water7,134396
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9490 Å2
ΔGint-41 kcal/mol
Surface area20100 Å2
Unit cell
Length a, b, c (Å)85.390, 85.390, 210.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-302-

CL

21B-403-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein tRNA (guanine-N(1)-)-methyltransferase


Mass: 27878.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Calditerrivibrio nitroreducens DSM 19672 (bacteria)
Gene: trmD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E4THH1

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Non-polymers , 5 types, 407 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


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


Mass: 18.015 Da / Num. of mol.: 396 / 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: 3.51 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein sample: 4 mg/mL TrmD in 50 mM HEPES buffer pH 7.4, 300 mM NaCl, 5% glycerol, 10 mM SAM, 20 mM MgCl2. Reservoir solution: 0.2 M sodium thiocyanate, 20% w/v PEG 3350 (JCSG+ screen 1-14).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.46522 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Oct 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.46522 Å / Relative weight: 1
ReflectionResolution: 2.19→45.79 Å / Num. obs: 40840 / % possible obs: 99.1 % / Redundancy: 8.75 % / Biso Wilson estimate: 32.88 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.133 / Net I/σ(I): 11.93
Reflection shellResolution: 2.19→2.32 Å / Redundancy: 5.67 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 6191 / CC1/2: 0.72 / Rrim(I) all: 1.018 / % possible all: 95.1

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8B1N

8b1n


Resolution: 2.19→44.83 Å / SU ML: 0.2483 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8238
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2088 2040 5 %
Rwork0.1665 38780 -
obs0.1687 40820 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.66 Å2
Refinement stepCycle: LAST / Resolution: 2.19→44.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3836 0 83 396 4315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074019
X-RAY DIFFRACTIONf_angle_d0.85735429
X-RAY DIFFRACTIONf_chiral_restr0.0525601
X-RAY DIFFRACTIONf_plane_restr0.0049694
X-RAY DIFFRACTIONf_dihedral_angle_d17.24821529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.240.32541240.26852359X-RAY DIFFRACTION92.79
2.24-2.290.31111290.26042444X-RAY DIFFRACTION96.29
2.29-2.360.30211320.22212517X-RAY DIFFRACTION98.04
2.36-2.430.22821350.20352556X-RAY DIFFRACTION99.52
2.43-2.50.28351350.18662572X-RAY DIFFRACTION100
2.5-2.590.2671350.18082556X-RAY DIFFRACTION99.93
2.59-2.70.21071340.17862579X-RAY DIFFRACTION99.96
2.7-2.820.19831350.1742575X-RAY DIFFRACTION99.82
2.82-2.970.25831370.18082601X-RAY DIFFRACTION100
2.97-3.150.22031370.17482607X-RAY DIFFRACTION99.96
3.15-3.40.2291370.16772603X-RAY DIFFRACTION99.96
3.4-3.740.18581380.14872628X-RAY DIFFRACTION99.96
3.74-4.280.1611400.13242647X-RAY DIFFRACTION100
4.28-5.390.14531410.12292681X-RAY DIFFRACTION100
5.39-44.830.20771510.17412855X-RAY DIFFRACTION99.77
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)
11.80471438648-0.221042169938-0.7023381060481.1940058990.4229279473252.94834446322-0.0493901987185-0.05027654878390.1524141803330.02485822510440.003344669606840.0693503258742-0.234924026305-0.1740702838190.04278972631780.244896206460.03360100415040.00038367163640.194551341713-0.001947010344840.250846216769-18.11601164524.030524096-8.15346452439
23.56656303688-5.574145897441.481145366538.83174495572-2.402351394770.6378561096530.08117536066670.448231976217-0.12455057392-1.244152661470.1224521633270.1276685101640.0745047316455-0.458169793167-0.177588831940.436619026116-3.56600870772E-50.002118785596650.5587490564690.006081939243590.31370512678-12.68953210212.9123613495-29.369463042
36.800193565625.2553543552-1.292246806555.23814386053-1.406338369462.10204595099-0.1007892664530.185484979615-0.176533755149-0.1845537314620.116589422974-0.01647580103460.168199624783-0.01011350920970.02212150029830.2372423103650.05369037697180.01041257339020.198232184754-0.0346409932020.232860562432-1.906961670440.167567973041-33.169091982
41.15987790842-0.0671791209758-0.5920608107021.35614718896-0.03848861900923.14991339436-0.0471822038667-0.03376093889550.1110790519520.04290408241220.000505603804177-0.119942099447-0.1807942560510.2496368732550.04029611748440.222694377125-0.0118349006122-0.003919535429210.2102371489560.006058859365530.2468789460095.0297219749318.548323813-17.7661757315
55.566115077755.593860267650.9659216710726.408676849730.5389506338680.4029079538220.589609059937-1.21375644290.2115435652591.64457309228-0.456575823520.292387878536-0.160260734172-0.303233326328-0.1093968829280.627510397790.07631088762550.03242104851750.641080540696-0.01718791955780.384620123488-4.2761674432913.96755571654.62772136731
62.04019104138-2.19865085408-0.951172951324.736685437181.10576937545.27917279451-0.450633451439-0.331599002353-0.4831197123980.6522063080690.1055896622490.2971553999330.9458103042860.2172093414210.328464355380.3936521084280.01004367671270.1057586278640.3456384779270.06047864606220.350624803249-18.84483783597.029629772278.98920543202
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 154 )
2X-RAY DIFFRACTION2chain 'A' and (resid 155 through 174 )
3X-RAY DIFFRACTION3chain 'A' and (resid 175 through 240 )
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 154 )
5X-RAY DIFFRACTION5chain 'B' and (resid 155 through 174 )
6X-RAY DIFFRACTION6chain 'B' and (resid 175 through 240 )

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