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- PDB-7myq: Crystal structure of a tRNA (guanine-N1)-methyltransferase from A... -

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Basic information

Entry
Database: PDB / ID: 7myq
TitleCrystal structure of a tRNA (guanine-N1)-methyltransferase from Acinetobacter baumannii
ComponentstRNA (guanine-N(1)-)-methyltransferaseTRNA (guanine9-N1)-methyltransferase
KeywordsTRANSFERASE / structural genomics / NIAID / tRNA / SAH / SAM / opportunistic pathogen / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / cytoplasm
Similarity search - Function
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
tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a tRNA (guanine-N1)-methyltransferase from Acinetobacter baumannii
Authors: Edwards, T.E. / Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionMay 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 (guanine-N(1)-)-methyltransferase
B: tRNA (guanine-N(1)-)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)57,8502
Polymers57,8502
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-21 kcal/mol
Surface area20810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.250, 66.250, 133.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 23 or (resid 24...
21(chain B and (resid 1 through 100 or (resid 101...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALGLYGLY(chain A and (resid 1 through 23 or (resid 24...AA1 - 239 - 31
12ARGARGARGARG(chain A and (resid 1 through 23 or (resid 24...AA24 - 2832 - 36
13HISHISGLUGLU(chain A and (resid 1 through 23 or (resid 24...AA0 - 2448 - 252
14HISHISGLUGLU(chain A and (resid 1 through 23 or (resid 24...AA0 - 2448 - 252
15HISHISGLUGLU(chain A and (resid 1 through 23 or (resid 24...AA0 - 2448 - 252
16HISHISGLUGLU(chain A and (resid 1 through 23 or (resid 24...AA0 - 2448 - 252
21VALVALGLUGLU(chain B and (resid 1 through 100 or (resid 101...BB1 - 1009 - 108
22GLNGLNALAALA(chain B and (resid 1 through 100 or (resid 101...BB101 - 102109 - 110
23VALVALGLNGLN(chain B and (resid 1 through 100 or (resid 101...BB1 - 2459 - 253
24VALVALGLNGLN(chain B and (resid 1 through 100 or (resid 101...BB1 - 2459 - 253
25VALVALGLNGLN(chain B and (resid 1 through 100 or (resid 101...BB1 - 2459 - 253
26VALVALGLNGLN(chain B and (resid 1 through 100 or (resid 101...BB1 - 2459 - 253

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Components

#1: Protein tRNA (guanine-N(1)-)-methyltransferase / TRNA (guanine9-N1)-methyltransferase / M1G-methyltransferase / tRNA [GM37] methyltransferase


Mass: 28924.916 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: trmD, ABC003_01337, ABUW_0322, EA686_14030, FDO31_01140, FJU79_00125, GNY86_14875, HYI42_11650
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0D5YDX5, tRNA (guanine37-N1)-methyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: AcbaC.00054.a.B1.PW38905 at 27 mg/mL against Morpheus condition D3 with 10% PEG 4000, 20% glycerol, 0.1 M MES/imidazole pH 6.5, 0.02 M each 1,6-hexanoediol, 1-butanol, 1,2-propanediol, 2- ...Details: AcbaC.00054.a.B1.PW38905 at 27 mg/mL against Morpheus condition D3 with 10% PEG 4000, 20% glycerol, 0.1 M MES/imidazole pH 6.5, 0.02 M each 1,6-hexanoediol, 1-butanol, 1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol, direct cryo, unique puck ID okj1-6, 319637d3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.55→46.85 Å / Num. obs: 18708 / % possible obs: 99.9 % / Redundancy: 6.368 % / Biso Wilson estimate: 60.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.051 / Χ2: 0.937 / Net I/σ(I): 24.4 / Num. measured all: 119128 / Scaling rejects: 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.55-2.626.4030.5843.528695135913580.9320.63699.9
2.62-2.696.3950.5074.048717136413630.9270.55299.9
2.69-2.776.4070.3615.68425131713150.9650.39399.8
2.77-2.856.4090.2856.918139127012700.9730.31100
2.85-2.946.4290.2148.927650119011900.9860.233100
2.94-3.056.4220.16611.237726120312030.9910.181100
3.05-3.166.4030.12115.137517117411740.9930.132100
3.16-3.296.4190.09219.116997109010900.9960.1100
3.29-3.446.3770.06625.446728105510550.9970.072100
3.44-3.616.3840.05330.276639104010400.9980.058100
3.61-3.86.3540.0532.8961329659650.9990.054100
3.8-4.036.3650.0439.2356848938930.9990.044100
4.03-4.316.3510.03543.5754628608600.9990.038100
4.31-4.666.3340.03148.9851758178170.9990.034100
4.66-5.16.3690.02951.8848477617610.9990.031100
5.1-5.76.30.0349.9741146536530.9990.033100
5.7-6.586.3170.02850.4136835835830.9990.03100
6.58-8.066.1740.02752.7631555115110.9990.029100
8.06-11.46.1370.02160.24246140140110.023100
11.4-46.855.7380.02459.0411822232060.9990.02692.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXdev-4224-000refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ual

1ual


Resolution: 2.55→46.85 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2293 1941 10.41 %
Rwork0.1932 16713 -
obs0.197 18654 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.11 Å2 / Biso mean: 75.7771 Å2 / Biso min: 40 Å2
Refinement stepCycle: final / Resolution: 2.55→46.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3470 0 0 49 3519
Biso mean---58.98 -
Num. residues----458
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1962X-RAY DIFFRACTION5.791TORSIONAL
12B1962X-RAY DIFFRACTION5.791TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.610.29481520.269611481300100
2.61-2.680.31421470.254911931340100
2.68-2.760.26921230.24312261349100
2.76-2.850.30061270.234711871314100
2.85-2.950.30341510.273411661317100
2.96-3.070.3041060.257412281334100
3.07-3.210.25771220.244812021324100
3.21-3.380.24181480.218511961344100
3.38-3.590.2411560.206811751331100
3.59-3.870.25251500.190411811331100
3.87-4.260.19651270.172512141341100
4.26-4.880.17241440.145911951339100
4.88-6.140.20911320.181312081340100
6.14-46.850.21561560.16551194135099
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)
13.45671.01641.73982.37010.22863.76310.1436-0.194-0.25650.14590.0512-0.48020.55440.3959-0.17890.37850.1-0.01250.39270.01570.339822.3574-3.37019.6717
24.59352.315-0.81852.7787-0.57082.2048-0.0393-0.1710.61940.0251-0.04130.1395-0.1553-0.06110.06850.42120.1355-0.0190.4332-0.04550.456620.49419.32765.5537
30.72870.680.99893.19010.46621.45290.33450.5589-0.1024-0.6379-0.8075-0.9463-0.24090.23110.36920.5733-0.1509-0.1790.94690.22431.620449.501732.4605-1.8762
42.357-3.18750.00215.3171.76378.7886-0.63810.23160.48240.60670.5684-0.4141-0.65830.59450.29111.00910.0987-0.28970.5559-0.10680.966829.901338.37591.2424
54.77020.1289-0.3455.3031-1.82433.0639-0.12680.20280.022-0.6523-0.2584-0.99480.52731.04930.3320.49630.22060.15630.85050.1660.680842.005110.8424-5.8486
65.56162.6621-0.09064.3567-0.41781.6604-0.12450.32450.3977-0.4688-0.0424-0.40910.11070.42590.20970.4980.16090.03990.53210.07310.364729.554710.2634-5.5584
75.32612.96711.70339.02860.3022.3333-0.42010.29230.4276-0.18530.40730.2411-0.35060.1426-0.00180.33480.0297-0.02380.37840.00210.23083.69834.0641-11.1479
85.4292.3133-3.63273.9922-2.05242.5162-1.39121.37870.2467-1.14681.04421.5330.6945-0.8932-0.18560.9251-0.1492-0.31630.63180.12090.6909-1.57278.5728-20.2084
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 91 )A0 - 91
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 182 )A92 - 182
3X-RAY DIFFRACTION3chain 'A' and (resid 183 through 204 )A183 - 204
4X-RAY DIFFRACTION4chain 'A' and (resid 205 through 244 )A205 - 244
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 108 )B1 - 108
6X-RAY DIFFRACTION6chain 'B' and (resid 109 through 192 )B109 - 192
7X-RAY DIFFRACTION7chain 'B' and (resid 193 through 234 )B193 - 234
8X-RAY DIFFRACTION8chain 'B' and (resid 235 through 245 )B235 - 245

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