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- PDB-7bu1: Crystal structure of TrmO from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 7bu1
TitleCrystal structure of TrmO from Pseudomonas aeruginosa
ComponentsPutative tRNA (Adenine(37)-N6)-methyltransferase
KeywordsTRANSFERASE / methyltransferase
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-ADENOSYLMETHIONINE / Methyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 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: Fan, 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)53,9034
Polymers53,1072
Non-polymers7972
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-27 kcal/mol
Surface area17820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.841, 69.980, 128.202
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
11THRTHRTYRTYR(chain 'A' and (resid 1 through 11 or resid 13...AA2 - 108 - 16
12SERSERMETMET(chain 'A' and (resid 1 through 11 or resid 13...AA13 - 1619 - 22
13PHEPHEPROPRO(chain 'A' and (resid 1 through 11 or resid 13...AA19 - 2225 - 28
14PROPROGLUGLU(chain 'A' and (resid 1 through 11 or resid 13...AA25 - 3631 - 42
15PROPROPROPRO(chain 'A' and (resid 1 through 11 or resid 13...AA39 - 4045 - 46
16GLUGLUGLNGLN(chain 'A' and (resid 1 through 11 or resid 13...AA45 - 6451 - 70
17LEULEUGLYGLY(chain 'A' and (resid 1 through 11 or resid 13...AA85 - 10891 - 114
18ALAALAALAALA(chain 'A' and (resid 1 through 11 or resid 13...AA111117
19LEULEUASPASP(chain 'A' and (resid 1 through 11 or resid 13...AA114 - 142120 - 148
110ASNASNALAALA(chain 'A' and (resid 1 through 11 or resid 13...AA145 - 148151 - 154
111PROPROALAALA(chain 'A' and (resid 1 through 11 or resid 13...AA153 - 167159 - 173
112HISHISARGARG(chain 'A' and (resid 1 through 11 or resid 13...AA170 - 173176 - 179
113GLNGLNASPASP(chain 'A' and (resid 1 through 11 or resid 13...AA176 - 189182 - 195
114GLUGLUALAALA(chain 'A' and (resid 1 through 11 or resid 13...AA198 - 228204 - 234
215THRTHRTYRTYR(chain 'B' and (resid 0 or resid 2 through 11...BB2 - 108 - 16
216SERSERMETMET(chain 'B' and (resid 0 or resid 2 through 11...BB13 - 1619 - 22
217PHEPHEPROPRO(chain 'B' and (resid 0 or resid 2 through 11...BB19 - 2225 - 28
218PROPROGLUGLU(chain 'B' and (resid 0 or resid 2 through 11...BB25 - 3631 - 42
219PROPROPROPRO(chain 'B' and (resid 0 or resid 2 through 11...BB39 - 4045 - 46
220GLUGLUGLNGLN(chain 'B' and (resid 0 or resid 2 through 11...BB45 - 6451 - 70
221LEULEUGLYGLY(chain 'B' and (resid 0 or resid 2 through 11...BB85 - 10891 - 114
222ALAALAALAALA(chain 'B' and (resid 0 or resid 2 through 11...BB111117
223LEULEUASPASP(chain 'B' and (resid 0 or resid 2 through 11...BB114 - 142120 - 148
224ASNASNALAALA(chain 'B' and (resid 0 or resid 2 through 11...BB145 - 148151 - 154
225PROPROALAALA(chain 'B' and (resid 0 or resid 2 through 11...BB153 - 167159 - 173
226HISHISARGARG(chain 'B' and (resid 0 or resid 2 through 11...BB170 - 173176 - 179
227GLNGLNASPASP(chain 'B' and (resid 0 or resid 2 through 11...BB176 - 189182 - 195
228GLUGLUALAALA(chain 'B' and (resid 0 or resid 2 through 11...BB198 - 228204 - 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-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


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


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.4 Å3/Da / Density % sol: 48.76 %
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: Jan 1, 2020
RadiationMonochromator: pixel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.49→47.27 Å / Num. obs: 18474 / % possible obs: 99.9 % / Redundancy: 12.9 % / Biso Wilson estimate: 47.13 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.058 / Rrim(I) all: 0.153 / Rsym value: 0.147 / Net I/σ(I): 16.2
Reflection shellResolution: 2.49→2.6 Å / Redundancy: 12.5 % / Rmerge(I) obs: 1.405 / Num. unique obs: 2045 / CC1/2: 0.802 / Rpim(I) all: 0.569 / Rrim(I) all: 1.465 / Rsym value: 1.405 / % possible all: 99.2

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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: 2.49→47.27 Å / SU ML: 0.3239 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.9161
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2731 922 5.01 %
Rwork0.227 17498 -
obs0.2292 18420 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.53 Å2
Refinement stepCycle: LAST / Resolution: 2.49→47.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3090 0 54 16 3160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063233
X-RAY DIFFRACTIONf_angle_d0.96094432
X-RAY DIFFRACTIONf_chiral_restr0.0537501
X-RAY DIFFRACTIONf_plane_restr0.0071573
X-RAY DIFFRACTIONf_dihedral_angle_d5.87791923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.630.34051280.28652432X-RAY DIFFRACTION99.3
2.63-2.790.28021300.25912463X-RAY DIFFRACTION99.88
2.79-3.010.31341300.27142475X-RAY DIFFRACTION100
3.01-3.310.34791300.24252470X-RAY DIFFRACTION99.96
3.31-3.790.27361320.22172491X-RAY DIFFRACTION99.89
3.79-4.770.21591320.19172525X-RAY DIFFRACTION99.92
4.77-47.270.27321400.22432642X-RAY DIFFRACTION99.75
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)
14.46510951016-0.2969414059782.866511099391.419663483450.6872546684424.742517774380.4315499547360.631585082428-0.577166962266-0.1694741184960.09269684450330.003942079363360.7840422655510.561322954056-0.4452357946770.4466202956330.0941392221056-0.08463221461590.346199329692-0.04373115922030.393462438876-5.07077487306-7.1932335783314.8174937261
24.97702018514-0.2021996264513.938958588952.88832966020.1031360995035.088158519350.1842956604980.353552713351-0.1865436252870.03036439194070.012915965048-0.168818230364-0.0697513974150.447319525456-0.1779972780330.4022451624310.0087047467910.02302695827940.3170201787730.003852630410690.313864098478-8.987570089280.23931572175813.9668012417
32.460810836740.3183222862430.8916706599956.709068718780.4023156350085.878263917210.1070044603270.1139704048130.07134976254750.130511644672-0.116264481706-0.735810453346-0.1716078459110.560156605620.0116507461280.3870019309-0.0888605012374-0.009679382890930.491745989260.0647912444120.40742187925510.02314749265.453532985529.6220164294
42.82829566792-0.6937063565353.457365769893.91567636051-2.278665145996.306177302080.0531617303342-0.630088011863-0.3592786290390.0771658538210.2922551957160.404739798180.130928660187-0.87168793778-0.3075334405120.331986389742-0.009850984448930.009378154216360.4074561399650.01780341701650.380792847193-27.085023410.0488460508617.02810073523
55.92825163501-1.827024170732.822702899841.616550386840.7627308727576.611864723240.4027676041560.326067278781-0.115042712929-0.405058865092-0.240512112851-0.2106668058860.100125755697-0.115700674335-0.03639852820070.357209720741-0.0260243024129-0.04515917961940.2580193421980.003587726398970.301718281901-18.8319500281-1.737590587955.80378804367
62.618336507020.2637938964323.196522969570.7456074225260.4575743904068.37225975922-0.07493611715070.138449899081-0.172733435714-0.002244386372520.06000179408640.00758338843556-0.3556851261730.5525624984670.01676442618760.340601206868-0.0177394626719-0.03952520082950.2371835817580.01021072872580.333694182733-18.94743424734.479463050871.04975838536
73.39707727272-0.42777220495-0.8673884792492.094291429331.960730724199.408106855270.06430176660560.04031844548950.0564136912227-0.0284283116290.2129778235940.08875022451480.1512152279840.0049712463115-0.2439101606990.3986522064550.02968566607070.002917466340870.2381056195750.01689265738260.366142059235-30.99367038573.18987747139-16.7398073383
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 61 )
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 155 )
3X-RAY DIFFRACTION3chain 'A' and (resid 156 through 229 )
4X-RAY DIFFRACTION4chain 'B' and (resid -1 through 47 )
5X-RAY DIFFRACTION5chain 'B' and (resid 48 through 109 )
6X-RAY DIFFRACTION6chain 'B' and (resid 110 through 160 )
7X-RAY DIFFRACTION7chain 'B' and (resid 161 through 229 )

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