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- PDB-5y0t: Crystal structure of Thermotoga maritima TmcAL bound with alpha-t... -

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Basic information

Entry
Database: PDB / ID: 5y0t
TitleCrystal structure of Thermotoga maritima TmcAL bound with alpha-thio ATP(Form II)
ComponentsThermotoga maritima TmcAL
KeywordsLIGASE / acetate ligase
Function / homology
Function and homology information


Ligases; Forming carbon-nitrogen bonds; Other carbon-nitrogen ligases / ligase activity, forming carbon-nitrogen bonds / tRNA modification / tRNA binding / ATP binding / cytoplasm
Similarity search - Function
tRNA(Met) cytidine acetate ligase / HIGH Nucleotidyl Transferase / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
ADENOSINE-5'-RP-ALPHA-THIO-TRIPHOSPHATE / tRNA(Met) cytidine acetate ligase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYamashita, S. / Tomita, K.
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: Acetate-dependent tRNA acetylation required for decoding fidelity in protein synthesis.
Authors: Taniguchi, T. / Miyauchi, K. / Sakaguchi, Y. / Yamashita, S. / Soma, A. / Tomita, K. / Suzuki, T.
History
DepositionJul 18, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / struct_keywords
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.2Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thermotoga maritima TmcAL
B: Thermotoga maritima TmcAL
C: Thermotoga maritima TmcAL
D: Thermotoga maritima TmcAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,75818
Polymers197,8684
Non-polymers2,89014
Water12,881715
1
A: Thermotoga maritima TmcAL
B: Thermotoga maritima TmcAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,35310
Polymers98,9342
Non-polymers1,4198
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-9 kcal/mol
Surface area33610 Å2
MethodPISA
2
C: Thermotoga maritima TmcAL
D: Thermotoga maritima TmcAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,4058
Polymers98,9342
Non-polymers1,4716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-11 kcal/mol
Surface area33700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.618, 97.813, 144.605
Angle α, β, γ (deg.)90.000, 99.280, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thermotoga maritima TmcAL


Mass: 49466.934 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1K1*PLUS
#2: Chemical
ChemComp-TAT / ADENOSINE-5'-RP-ALPHA-THIO-TRIPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O12P3S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 715 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsOur sequence is based on WP_024103782.1.

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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: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Tris, PEG8000, NaCl

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 170997 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 26.84 Å2 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.122 / Χ2: 0.942 / Net I/σ(I): 14.32
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) all% possible all
1.9-1.951.4151.34124351.53296.6
1.95-21.1271.77121531.21497.2
2-2.060.8722.33118100.9497.3
2.06-2.120.6652.99116080.7297.5
2.12-2.190.5263.81111820.56797.6
2.19-2.270.4084.83108410.4497.9
2.27-2.360.3245.89104770.35197.9
2.36-2.450.2647.41101220.28497.9
2.45-2.560.2258.5996970.24398.3
2.56-2.690.1899.9993390.20498.3
2.69-2.830.13913.5388280.1598.5
2.83-30.11515.8384450.12498.7
3-3.210.08820.6379000.09598.8
3.21-3.470.06726.0973850.07399
3.47-3.80.04835.3868220.05299.1
3.8-4.250.03843.3562150.04199.2
4.25-4.910.03251.7454500.03499.4
4.91-6.010.03545.6346400.03899.5
6.01-8.50.03150.8736290.03399.4
8.50.02170.6920190.02398.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y0R

5y0r


Resolution: 1.9→47.571 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.23
RfactorNum. reflection% reflection
Rfree0.2033 8549 5 %
Rwork0.1704 --
obs0.1721 170978 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 170.5 Å2 / Biso mean: 36.97 Å2 / Biso min: 13.39 Å2
Refinement stepCycle: final / Resolution: 1.9→47.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13541 0 176 715 14432
Biso mean--37.63 35.56 -
Num. residues----1654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714007
X-RAY DIFFRACTIONf_angle_d1.09618812
X-RAY DIFFRACTIONf_chiral_restr0.0452009
X-RAY DIFFRACTIONf_plane_restr0.0062394
X-RAY DIFFRACTIONf_dihedral_angle_d14.6055296
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9001-1.92170.33912810.30935352563396
1.9217-1.94430.33042780.28355282556097
1.9443-1.9680.31462790.27045300557997
1.968-1.99290.26482820.24975353563597
1.9929-2.01910.28312820.23715360564297
2.0191-2.04680.25762820.22475358564097
2.0468-2.0760.25592820.21325360564298
2.076-2.1070.24012810.20845335561697
2.107-2.13990.23722830.20725370565397
2.1399-2.1750.26082830.20355386566998
2.175-2.21250.25282820.18995353563598
2.2125-2.25270.22752820.18395364564698
2.2527-2.29610.21372860.17535419570598
2.2961-2.34290.22662810.17675353563498
2.3429-2.39390.22452870.16455438572598
2.3939-2.44960.20142830.1655382566598
2.4496-2.51080.22682860.16845431571798
2.5108-2.57870.21672830.16615390567398
2.5787-2.65460.20262870.16915435572299
2.6546-2.74030.20382830.16675395567898
2.7403-2.83820.21032880.16325460574899
2.8382-2.95180.21132860.17055440572699
2.9518-3.08610.22162880.18085464575299
3.0861-3.24880.21462880.17615487577599
3.2488-3.45230.20182860.17795433571999
3.4523-3.71870.18342910.16565521581299
3.7187-4.09280.17562890.14535497578699
4.0928-4.68460.14912920.12765535582799
4.6846-5.90030.16162910.14095527581899
5.9003-47.58640.15972970.14745649594699
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)
11.0727-0.16830.44280.9110.05691.6006-0.01240.01370.04960.00070.0223-0.0518-0.06740.1676-0.00830.0999-0.0153-0.00670.1763-0.00020.172854.933377.4502126.4656
22.4682-0.40410.46674.7522-0.37991.78470.01940.17340.6176-0.04130.0057-0.0249-0.43870.1908-0.06510.2698-0.0468-0.00630.22210.01450.3150.92398.7897132.7749
30.43750.1170.09210.8085-0.11771.4018-0.00570.02680.0597-0.0742-0.01520.0355-0.15270.08970.01070.1406-0.0166-0.01280.16050.00990.175848.26678.3682113.1998
42.1419-0.21140.33620.41720.30611.43810.05710.1407-0.0155-0.3107-0.06220.04710.0377-0.03860.00720.38050.0432-0.04010.19020.0290.197231.353883.808969.7985
54.89430.6336-2.63726.1869-0.74072.6687-0.46840.0694-0.75920.16030.03370.4670.6155-0.13530.40880.53210.0113-0.06210.2967-0.04660.421614.719268.838173.0667
60.6585-0.18870.56721.2948-0.39481.65390.091-0.00960.0238-0.1995-0.05090.0216-0.07810.0019-0.02630.24490.0036-0.03350.18360.02860.179236.511683.34683.6342
72.2828-0.1684-0.49350.55980.15771.28-0.0869-0.17060.00330.040.03670.06370.03190.05450.0510.15950.006-0.00210.19340.02770.241421.512433.8739145.8415
81.6666-1.95731.3223.6905-1.52593.13130.02-0.03720.2181-0.04170.0022-0.1137-0.31360.0687-0.00620.1557-0.02890.04280.19810.00650.34615.225847.6946137.5219
91.04210.1926-0.64721.2572-0.37240.9057-0.09110.0027-0.0654-0.01540.05220.08340.088-0.00760.03680.14210.0033-0.01260.16620.01270.196330.623434.4985134.1159
101.19190.0413-0.1680.96020.39031.6988-0.06910.0936-0.1011-0.37010.0222-0.22750.29910.28060.03460.34220.06140.07690.2304-0.00220.19162.319742.5593100.0895
113.51320.57341.23390.50240.04870.97290.27980.0452-1.6118-0.18930.0807-0.45491.10510.4131-0.10141.21230.17510.15320.387-0.0960.88562.981121.085293.7985
120.50810.1209-0.34580.9561-0.55190.9128-0.06650.0235-0.0836-0.29340.0115-0.02690.24750.0170.03750.25730.017-0.00450.1712-0.01190.169651.283440.7509109.9771
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:107)A1 - 107
2X-RAY DIFFRACTION2(chain A and resid 108:196)A108 - 196
3X-RAY DIFFRACTION3(chain A and resid 206:423)A206 - 423
4X-RAY DIFFRACTION4(chain B and resid 1:107)B1 - 107
5X-RAY DIFFRACTION5(chain B and resid 108:195)B108 - 195
6X-RAY DIFFRACTION6(chain B and resid 205:423)B205 - 423
7X-RAY DIFFRACTION7(chain C and resid 1:107)C1 - 107
8X-RAY DIFFRACTION8(chain C and resid 108:194)C108 - 194
9X-RAY DIFFRACTION9(chain C and resid 206:423)C206 - 423
10X-RAY DIFFRACTION10(chain D and resid 1:107)D1 - 107
11X-RAY DIFFRACTION11(chain D and resid 108:195)D108 - 195
12X-RAY DIFFRACTION12(chain D and resid 205:423)D205 - 423

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