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- PDB-7btu: Crystal structure of TrmO from P. areuginosa -

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Basic information

Entry
Database: PDB / ID: 7btu
TitleCrystal structure of TrmO from P. areuginosa
ComponentsPutative tRNA (Adenine(37)-N6)-methyltransferase
KeywordsTRANSFERASE / methyl-transferase
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
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsFan, C.P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31570762 China
CitationJournal: To Be Published
Title: Crystal structure of TrmO
Authors: Fan, C.P.
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

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Assembly

Deposited unit
A: Putative tRNA (Adenine(37)-N6)-methyltransferase
B: Putative tRNA (Adenine(37)-N6)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)53,1072
Polymers53,1072
Non-polymers00
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-33 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.903, 70.723, 127.773
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
11METMETTYRTYR(chain 'A' and (resid -3 or resid 1 through 11...AA1 - 107 - 16
12SERSERILEILE(chain 'A' and (resid -3 or resid 1 through 11...AA13 - 2119 - 27
13GLNGLNLEULEU(chain 'A' and (resid -3 or resid 1 through 11...AA24 - 6130 - 67
14SERSERASPASP(chain 'A' and (resid -3 or resid 1 through 11...AA84 - 12990 - 135
15PROPROASPASP(chain 'A' and (resid -3 or resid 1 through 11...AA132 - 142138 - 148
16ASNASNILEILE(chain 'A' and (resid -3 or resid 1 through 11...AA145 - 147151 - 153
17ALAALAGLNGLN(chain 'A' and (resid -3 or resid 1 through 11...AA150 - 162156 - 168
18ARGARGALAALA(chain 'A' and (resid -3 or resid 1 through 11...AA165 - 167171 - 173
19HISHISVALVAL(chain 'A' and (resid -3 or resid 1 through 11...AA170 - 178176 - 184
110LEULEUGLUGLU(chain 'A' and (resid -3 or resid 1 through 11...AA181 - 183187 - 189
111LEULEUALAALA(chain 'A' and (resid -3 or resid 1 through 11...AA186 - 187192 - 193
112PROPROPROPRO(chain 'A' and (resid -3 or resid 1 through 11...AA199205
113ARGARGALAALA(chain 'A' and (resid -3 or resid 1 through 11...AA202 - 228208 - 234
214METMETTYRTYR(chain 'B' and (resid -2 or resid 1 through 11...BB1 - 107 - 16
215SERSERILEILE(chain 'B' and (resid -2 or resid 1 through 11...BB13 - 2119 - 27
216GLNGLNLEULEU(chain 'B' and (resid -2 or resid 1 through 11...BB24 - 6130 - 67
217SERSERASPASP(chain 'B' and (resid -2 or resid 1 through 11...BB84 - 12990 - 135
218PROPROASPASP(chain 'B' and (resid -2 or resid 1 through 11...BB132 - 142138 - 148
219ASNASNILEILE(chain 'B' and (resid -2 or resid 1 through 11...BB145 - 147151 - 153
220ALAALAGLNGLN(chain 'B' and (resid -2 or resid 1 through 11...BB150 - 162156 - 168
221ARGARGALAALA(chain 'B' and (resid -2 or resid 1 through 11...BB165 - 167171 - 173
222HISHISVALVAL(chain 'B' and (resid -2 or resid 1 through 11...BB170 - 178176 - 184
223LEULEUGLUGLU(chain 'B' and (resid -2 or resid 1 through 11...BB181 - 183187 - 189
224LEULEUALAALA(chain 'B' and (resid -2 or resid 1 through 11...BB186 - 187192 - 193
225PROPROPROPRO(chain 'B' and (resid -2 or resid 1 through 11...BB199205
226ARGARGALAALA(chain 'B' and (resid -2 or resid 1 through 11...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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 297 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 PILATUS 2M / Detector: PIXEL / Date: Nov 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.91→47.41 Å / Num. obs: 40832 / % possible obs: 99.8 % / Redundancy: 13.1 % / Biso Wilson estimate: 22.79 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.049 / Rrim(I) all: 0.18 / Rsym value: 0.173 / Net I/σ(I): 11.1
Reflection shellResolution: 1.91→1.95 Å / Redundancy: 13 % / Rmerge(I) obs: 1.398 / Num. unique obs: 2645 / CC1/2: 0.798 / Rpim(I) all: 0.4 / Rrim(I) all: 1.455 / Rsym value: 1.398 / % possible all: 98

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Processing

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

1xqb


Resolution: 1.91→47.41 Å / SU ML: 0.2172 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.7049
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2283 1988 4.88 %
Rwork0.1861 38757 -
obs0.1881 40745 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.17 Å2
Refinement stepCycle: LAST / Resolution: 1.91→47.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3253 0 0 306 3559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01533348
X-RAY DIFFRACTIONf_angle_d1.30664579
X-RAY DIFFRACTIONf_chiral_restr0.0967507
X-RAY DIFFRACTIONf_plane_restr0.01605
X-RAY DIFFRACTIONf_dihedral_angle_d3.66472331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.960.33661490.2892656X-RAY DIFFRACTION98.46
1.96-2.010.24581530.21162730X-RAY DIFFRACTION100
2.01-2.070.24291490.2042699X-RAY DIFFRACTION99.82
2.07-2.140.29741350.20182756X-RAY DIFFRACTION99.97
2.14-2.210.24391490.19672758X-RAY DIFFRACTION99.9
2.21-2.30.25941530.20232692X-RAY DIFFRACTION99.89
2.3-2.40.22521250.17722781X-RAY DIFFRACTION99.93
2.4-2.530.21581270.18282779X-RAY DIFFRACTION100
2.53-2.690.2491290.18432766X-RAY DIFFRACTION100
2.69-2.90.24041400.19752766X-RAY DIFFRACTION99.79
2.9-3.190.25651360.18742804X-RAY DIFFRACTION100
3.19-3.650.20321400.17352801X-RAY DIFFRACTION99.93
3.65-4.60.18341510.15382810X-RAY DIFFRACTION99.36
4.6-47.410.21911520.19132959X-RAY DIFFRACTION99.33
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)
12.090726645590.4540401439640.7274550025521.42819531753-0.2939880743741.782974476940.08946811483120.138863933541-0.195253047281-0.008860297014620.01749359076740.02633945917860.2446185039180.0444278009148-0.08925745084780.116801232870.0266401625816-0.01220145968830.126313941972-0.0208505528010.153689334593-7.09452851805-8.2917474024314.9253395038
25.010919088190.344389949901-0.3047531313254.106048806040.09639086085471.94512296912-0.195695161911-0.6062743048970.1152706349650.5539504983870.298021083447-0.363014972433-0.1917543444620.190010254312-0.08119139390640.3114386007260.0474604802767-0.02935235608070.345646342239-0.05668830644250.207102276432-18.07779008122.6804340899822.2396310065
31.320481959690.1845147156161.165729725190.285006794048-0.2370990816511.91303112399-0.03096996238380.1843680841530.00201990589781-0.0188101536539-0.00885167064712-0.0740713965581-0.07397809668980.3382558068770.03731296999120.1371034049730.00636681973520.01686774275230.216203250763-0.01363792592770.1668770194811.93511489690.10952261668217.1902805602
42.160138434781.608904033290.08476780322495.69377103150.1432926144443.712920373350.114833118970.07162284445040.1720967241110.279188470701-0.20502321468-0.0597599252003-0.8297225753610.2491654257670.06963154143380.284248231063-0.01627390533310.0007438014692650.188649434248-0.01373478446920.1518417758817.068112484797.9894111085332.6843585569
53.94087158876-2.451873441792.192755254494.88760945408-2.286735205173.442564333990.270647914443-0.174905798342-0.632062420103-0.05391026340860.07831425671970.2868305199590.4812439764730.0792114488761-0.1878004705240.236683682656-0.0338957468588-0.0305897844720.2342752363870.02027842722520.279432096979-21.1040104892-13.260039387920.0729561599
62.235391261260.2984034863770.1856814775931.92926033925-0.1264126236663.04384192666-0.0117793322785-0.06975321381710.000338262609421-0.0993926506919-0.02435067355330.136835000964-0.149997145849-0.1611518744730.008340767831360.1438512101030.00816814087377-0.0190964300530.1439860271090.01043497615850.165737177673-25.77512652074.457561808246.40675859047
76.18985166171-2.70077529857-2.467921851035.108589570522.121634368313.837397640210.08806340282880.739258277801-0.706196559495-0.0702706877342-0.04268496957030.4133042553190.213632850033-0.09906952323590.0002403705243790.3069813487240.0191577535511-0.1019915175520.252823617644-0.1302241396210.302571438043-14.1917730454-14.35062250922.06742981192
80.7295475103550.7733273134930.4647594033482.123649412630.2727037755512.30570371666-0.01227185391650.03506575291610.0453734997649-0.0104949687597-0.01744880241210.0937035111465-0.1479566547780.05941268904860.0267253297220.125803751383-0.00850808540349-0.01778270183140.1261155623380.003335127784540.152082580475-22.263427414.241559364137.95395632799
92.82944081431-1.860030251452.945203760931.10023237946-1.117983065853.812048408470.356119253670.7573096618070.00683681939899-0.351756340218-0.192937110255-0.08736856585110.1952810280791.03744908134-0.1082444124470.270243622709-0.00374363660940.01371005142580.3414461240.01133745230290.182434128583-12.02373253172.85654836737-9.91804923123
105.88610706449-0.894888162157-4.053939637284.61244605104-1.730771023328.147683247670.07799513137990.529079418017-0.11787445055-0.232539209485-0.0559725520660.492606596797-0.282483119248-1.087410699680.07291061556210.175322895260.0612489124641-0.03490993323760.2112129257690.006422982186590.24932327711-39.37574425729.54831037091-14.6189231423
118.06046458589-1.53328933217-2.203077528955.184840545151.019487412488.99836564242-0.2213000433540.1294256992290.3568984715280.1266555641270.202815261568-0.228233691206-0.2709517365510.455990013752-0.03858351387650.183323277115-0.000233741375519-0.06898260703490.1146957097210.01007547192460.119735341301-28.09433602537.48741017535-10.4680978751
122.94714879033-1.01201001126-2.490375221432.04479554381.250389689777.73431231928-0.01803185733790.0810921735888-0.1238498148540.005226791690470.0264398747901-0.08510087477830.3932611326070.202067754750.04355219551070.2134649321530.0272176817142-0.04153774320490.15804741868-0.009482244626710.194680512797-29.032325395-1.38913123756-18.85950287
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 61 )
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 98 )
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 188 )
4X-RAY DIFFRACTION4chain 'A' and (resid 189 through 230 )
5X-RAY DIFFRACTION5chain 'B' and (resid -2 through 8 )
6X-RAY DIFFRACTION6chain 'B' and (resid 9 through 61 )
7X-RAY DIFFRACTION7chain 'B' and (resid 62 through 95 )
8X-RAY DIFFRACTION8chain 'B' and (resid 96 through 138 )
9X-RAY DIFFRACTION9chain 'B' and (resid 139 through 160 )
10X-RAY DIFFRACTION10chain 'B' and (resid 161 through 174 )
11X-RAY DIFFRACTION11chain 'B' and (resid 175 through 188 )
12X-RAY DIFFRACTION12chain 'B' and (resid 189 through 229 )

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