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- PDB-7btz: Crystal structure of TrmO -

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Basic information

Entry
Database: PDB / ID: 7btz
TitleCrystal structure of TrmO
ComponentsPutative tRNA (Adenine(37)-N6)-methyltransferase
KeywordsTRANSFERASE / methyltranserase
Function / homology
Function and homology information


Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation
Similarity search - Function
TrmO, C-terminal / TrmO C-terminal domain / Uncharacterised protein family UPF0066, conserved site / TsaA-like domain signature. / TrmO-like, N-terminal domain / YaeB-like superfamily / YaeB, N-terminal domain superfamily / YaeB-like / tRNA-methyltransferase O / TsaA-like domain profile.
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / tRNA (Adenine(37)-N6)-methyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFan, C.P. / Wang, L. / Hu, W.H. / Yang, C.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31570762 China
CitationJournal: To Be Published
Title: Crystal structure of TrmO from Pseudomonas aeruginosa
Authors: Fa, C.P. / Wang, L. / Hu, W.H. / Yang, C.W.
History
DepositionApr 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Putative tRNA (Adenine(37)-N6)-methyltransferase
B: Putative tRNA (Adenine(37)-N6)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8754
Polymers53,1072
Non-polymers7692
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-31 kcal/mol
Surface area18320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.913, 69.931, 127.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

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
11METMETPHEPHE(chain 'A' and (resid 1 through 42 or resid 44...AA1 - 417 - 47
12VALVALLEULEU(chain 'A' and (resid 1 through 42 or resid 44...AA44 - 5050 - 56
13VALVALGLNGLN(chain 'A' and (resid 1 through 42 or resid 44...AA53 - 6459 - 70
14ARGARGLEULEU(chain 'A' and (resid 1 through 42 or resid 44...AA71 - 7277 - 78
15LEULEUASNASN(chain 'A' and (resid 1 through 42 or resid 44...AA85 - 14591 - 151
16PROPROGLNGLN(chain 'A' and (resid 1 through 42 or resid 44...AA151 - 162157 - 168
17GLNGLNALAALA(chain 'A' and (resid 1 through 42 or resid 44...AA166 - 167172 - 173
18HISHISALAALA(chain 'A' and (resid 1 through 42 or resid 44...AA170 - 187176 - 193
19PROPROPROPRO(chain 'A' and (resid 1 through 42 or resid 44...AA199205
110ARGARGALAALA(chain 'A' and (resid 1 through 42 or resid 44...AA202 - 228208 - 234
211METMETPHEPHE(chain 'B' and (resid 1 through 42 or resid 44...BB1 - 417 - 47
212VALVALLEULEU(chain 'B' and (resid 1 through 42 or resid 44...BB44 - 5050 - 56
213VALVALGLNGLN(chain 'B' and (resid 1 through 42 or resid 44...BB53 - 6459 - 70
214LEULEULYSLYS(chain 'B' and (resid 1 through 42 or resid 44...BB72 - 7378 - 79
215LEULEUASNASN(chain 'B' and (resid 1 through 42 or resid 44...BB85 - 14591 - 151
216PROPROGLNGLN(chain 'B' and (resid 1 through 42 or resid 44...BB151 - 162157 - 168
217GLNGLNALAALA(chain 'B' and (resid 1 through 42 or resid 44...BB166 - 167172 - 173
218HISHISALAALA(chain 'B' and (resid 1 through 42 or resid 44...BB170 - 187176 - 193
219PROPROPROPRO(chain 'B' and (resid 1 through 42 or resid 44...BB199205
220ARGARGALAALA(chain 'B' and (resid 1 through 42 or resid 44...BB202 - 228208 - 234

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Components

#1: Protein Putative tRNA (Adenine(37)-N6)-methyltransferase / TrmO / UPF0066 protein / tRNA (N6-threonylcarbamoyladenosine(37)-N6)-methyltransferase TrmO


Mass: 26553.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: rcsF, tsaA, tsaA_3, C0044_25415, CAZ10_20550, DT376_18640, DY930_12780, E4V10_08585, IPC1481_19460, IPC1509_00145, IPC47_19985, IPC669_23210, PAMH19_1683, RW109_RW109_02414
Production host: Escherichia coli (E. coli) / References: UniProt: A0A080VNW8
#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.: 69 / 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: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES (pH 7.5), 1.2 M K2HPO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 16, 2019
RadiationMonochromator: pixel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→19.74 Å / Num. obs: 20854 / % possible obs: 99.8 % / Redundancy: 13.1 % / Biso Wilson estimate: 37.96 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.205 / Rpim(I) all: 0.058 / Rrim(I) all: 0.213 / Rsym value: 0.205 / Net I/σ(I): 12.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 13.7 % / Rmerge(I) obs: 1.547 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2139 / CC1/2: 0.726 / Rpim(I) all: 0.431 / Rrim(I) all: 1.607 / Rsym value: 1.547 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XQB

1xqb


Resolution: 2.4→19.74 Å / SU ML: 0.2551 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.0126
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2534 1051 5.05 %
Rwork0.2033 19758 -
obs0.2059 20809 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.59 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3190 0 52 69 3311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00363333
X-RAY DIFFRACTIONf_angle_d0.7514557
X-RAY DIFFRACTIONf_chiral_restr0.0474505
X-RAY DIFFRACTIONf_plane_restr0.0059592
X-RAY DIFFRACTIONf_dihedral_angle_d6.05441998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.510.30121260.25352425X-RAY DIFFRACTION99.96
2.51-2.640.32691220.23912434X-RAY DIFFRACTION100
2.64-2.810.291240.2282419X-RAY DIFFRACTION99.96
2.81-3.020.28171250.22252464X-RAY DIFFRACTION100
3.02-3.320.27891220.20972460X-RAY DIFFRACTION99.96
3.32-3.80.2281490.19562464X-RAY DIFFRACTION99.96
3.8-4.780.22371340.17242486X-RAY DIFFRACTION99.92
4.78-19.740.24271490.20182606X-RAY DIFFRACTION99.96
Refinement TLS params.Method: refined / Origin x: -13.1679259184 Å / Origin y: 0.605865644736 Å / Origin z: 8.60435592009 Å
111213212223313233
T0.215711615501 Å20.0100218321985 Å20.0217034274258 Å2-0.190197387249 Å2-0.0360612406784 Å2--0.239731531177 Å2
L1.78642573065 °20.00944422865296 °22.28773125372 °2-0.430858668655 °20.0186990964033 °2--3.48694161343 °2
S0.0699451118786 Å °0.153977787486 Å °-0.119965853806 Å °0.0254948535088 Å °0.0548129590402 Å °-0.0565433278928 Å °-0.0203103279352 Å °0.259789793267 Å °-0.0882547043141 Å °
Refinement TLS groupSelection details: all

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