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

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Basic information

Entry
Database: PDB / ID: 7mys
TitleCrystal structure of a tRNA (guanine-N1)-methyltransferase from Acinetobacter baumannii AB5075-UW bound to S-adenosyl homocysteine
ComponentstRNA (guanine-N(1)-)-methyltransferase
KeywordsTRANSFERASE / NIH / structural genomics / SAH / SAM / TrmD / opportunistic pathogen / tRNA biogenesis / 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
S-ADENOSYL-L-HOMOCYSTEINE / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 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 AB5075-UW bound to S-adenosyl homocysteine
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6194
Polymers57,8502
Non-polymers7692
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-25 kcal/mol
Surface area19990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.960, 65.960, 132.590
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 0 through 23 or (resid 24...
21(chain B and (resid 0 through 103 or (resid 104...

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
11HISHISGLYGLY(chain A and (resid 0 through 23 or (resid 24...AA0 - 238 - 31
12ARGARGLYSLYS(chain A and (resid 0 through 23 or (resid 24...AA24 - 2732 - 35
13HISHISSAHSAH(chain A and (resid 0 through 23 or (resid 24...AA - C0 - 3018
14HISHISSAHSAH(chain A and (resid 0 through 23 or (resid 24...AA - C0 - 3018
15HISHISSAHSAH(chain A and (resid 0 through 23 or (resid 24...AA - C0 - 3018
16HISHISSAHSAH(chain A and (resid 0 through 23 or (resid 24...AA - C0 - 3018
21HISHISVALVAL(chain B and (resid 0 through 103 or (resid 104...BB0 - 1038 - 111
22GLNGLNGLNGLN(chain B and (resid 0 through 103 or (resid 104...BB104 - 105112 - 113
23HISHISSAHSAH(chain B and (resid 0 through 103 or (resid 104...BB - D0 - 3018
24HISHISSAHSAH(chain B and (resid 0 through 103 or (resid 104...BB - D0 - 3018
25HISHISSAHSAH(chain B and (resid 0 through 103 or (resid 104...BB - D0 - 3018
26HISHISSAHSAH(chain B and (resid 0 through 103 or (resid 104...BB - D0 - 3018

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Components

#1: Protein tRNA (guanine-N(1)-)-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: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.53 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 26 mg/mL with 6 mM GMP and 6 mM SAH against Morpheus condition F2 with 10% PEG 8000, 20% ethylene glycol, 0.1 M MES/imidazole pH 6.5, 0.02 M each glucose, ...Details: AcbaC.00054.a.B1.PW38905 at 26 mg/mL with 6 mM GMP and 6 mM SAH against Morpheus condition F2 with 10% PEG 8000, 20% ethylene glycol, 0.1 M MES/imidazole pH 6.5, 0.02 M each glucose, mannose, galactose, fucose, xylose, acetyl-glucosamine, direct cryo, unique puck ID okj1-10, crystal tracking ID 319640f2

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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: 2.4→46.64 Å / Num. obs: 22187 / % possible obs: 100 % / Redundancy: 6.328 % / Biso Wilson estimate: 56.43 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.043 / Χ2: 0.936 / Net I/σ(I): 25.84 / Num. measured all: 140392
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
2.4-2.466.3870.5243.6910564165416540.910.571100
2.46-2.536.4140.4234.610263160016000.9490.461100
2.53-2.66.3860.36.299764152915290.9780.326100
2.6-2.686.40.267.29600150015000.9730.283100
2.68-2.776.4140.1949.549313145214520.9860.211100
2.77-2.876.4120.14912.029285144814480.9910.162100
2.87-2.986.3970.11614.938540133513350.9950.126100
2.98-3.16.380.08719.038390131513150.9970.095100
3.1-3.246.3610.06825.098015126012600.9970.074100
3.24-3.396.390.04831.77572118511850.9990.053100
3.39-3.586.3220.0437.387334116011600.9990.043100
3.58-3.796.2960.03543.156844108710870.9990.038100
3.79-4.066.2630.03247.646401102210220.9990.035100
4.06-4.386.2450.02951.0859399519510.9990.031100
4.38-4.86.2590.02754.7154588728720.9990.03100
4.8-5.376.1490.02655.0448587907900.9990.028100
5.37-6.26.1550.02554.7743647097090.9990.027100
6.2-7.596.1290.02655.9936225915910.9990.029100
7.59-10.736.060.02160.4628364684680.9990.023100
10.73-46.645.5210.02357.9314302672590.9990.02697

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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: 2.4→46.64 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2252 2057 9.29 %
Rwork0.181 20075 -
obs0.185 22132 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.23 Å2 / Biso mean: 71.293 Å2 / Biso min: 38.32 Å2
Refinement stepCycle: final / Resolution: 2.4→46.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3601 0 52 59 3712
Biso mean--58.77 58.47 -
Num. residues----478
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2110X-RAY DIFFRACTION4.768TORSIONAL
12B2110X-RAY DIFFRACTION4.768TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4-2.460.36091810.267113221503
2.46-2.520.27971400.248612991439
2.52-2.590.29321350.233413311466
2.59-2.660.26811530.225113111464
2.66-2.750.26991370.222513691506
2.75-2.850.2821380.235713071445
2.85-2.960.32571060.255413741480
2.96-3.090.27661260.226613451471
3.09-3.260.26071460.204813171463
3.26-3.460.24131250.197213581483
3.46-3.730.22451230.185113501473
3.73-4.10.22931220.162313591481
4.1-4.70.15951240.145613501474
4.7-5.910.19151430.166113501493
5.92-46.640.20061580.14613331491
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)
14.65121.30741.61032.15360.22993.98670.0097-0.2874-0.2090.11640.0453-0.53430.42040.4867-0.04880.51720.17180.0290.52910.02680.420925.1229-4.00537.4768
23.49251.3422-0.55522.1646-0.30243.02450.0067-0.2570.15180.1279-0.0368-0.0220.13690.10620.03640.39730.11340.00490.4117-0.01010.346118.32834.5557.7742
33.84123.1361-1.44096.2523-1.93573.7218-0.0174-0.63480.81980.79040.0725-0.3627-0.63830.9593-0.12780.76850.0042-0.04290.8082-0.24270.88233.040725.3137.6888
40.2921-0.36330.08890.4067-0.27911.1676-0.28520.17860.3293-0.0407-1.08180.9672-0.03591.18311.42190.7995-0.48770.27111.2221-0.31851.686450.42733.55450.5268
51.0021-2.4993-1.01335.57863.66245.5238-0.44360.05020.7343-0.61920.6547-0.4762-1.70560.5993-0.32941.0198-0.12700.5224-0.18491.06129.585537.52872.13
65.06260.4447-1.25824.4795-0.50733.16630.0002-0.14560.0397-0.2248-0.0452-0.71270.21430.95890.00480.34490.08020.03080.68490.01490.507939.881711.7574-5.9795
71.2421.296-0.51191.3085-1.03035.2088-0.25381.1736-0.2496-0.84570.8074-0.35630.20670.2602-0.55590.7523-0.1066-0.04790.8418-0.12240.65617.13453.1822-13.2431
83.53062.82842.47986.22240.5153.686-0.30160.20180.389-0.48810.15840.7453-0.1498-0.12690.15440.41050.05130.03760.4577-0.02740.39172.92142.5608-10.626
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 63 )A0 - 63
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 159 )A64 - 159
3X-RAY DIFFRACTION3chain 'A' and (resid 160 through 185 )A160 - 185
4X-RAY DIFFRACTION4chain 'A' and (resid 186 through 204 )A186 - 204
5X-RAY DIFFRACTION5chain 'A' and (resid 205 through 244 )A205 - 244
6X-RAY DIFFRACTION6chain 'B' and (resid 0 through 159 )B0 - 159
7X-RAY DIFFRACTION7chain 'B' and (resid 160 through 183 )B160 - 183
8X-RAY DIFFRACTION8chain 'B' and (resid 184 through 245 )B184 - 245

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