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- PDB-5y0q: Crystal structure of BsTmcAL bound with AMPCPP -

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Basic information

Entry
Database: PDB / ID: 5y0q
TitleCrystal structure of BsTmcAL bound with AMPCPP
ComponentsUPF0348 protein B4417_3650
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
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / tRNA(Met) cytidine acetate ligase / tRNA(Met) cytidine acetate ligase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0348 protein B4417_3650
B: UPF0348 protein B4417_3650
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,1844
Polymers98,1742
Non-polymers1,0102
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-11 kcal/mol
Surface area33760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.995, 68.013, 211.672
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UPF0348 protein B4417_3650


Mass: 49086.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The gene was cloned into pET15b with NdeI and XhoI site, and expressed as a N-terminally His-tagged protein.
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_3650 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A164SIT4, UniProt: O34513*PLUS
#2: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Tris-HCl, PEG400, KCl, MgCl2

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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
Reflection twinOperator: -k,-h,-l / Fraction: 0.5
ReflectionResolution: 2.1→50 Å / Num. obs: 58350 / % possible obs: 99.95 % / Observed criterion σ(I): -3 / Redundancy: 13.16 % / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.015 / Χ2: 1.038 / Net I/σ(I): 28.48
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) all% possible all
2.1-2.1412.891.8131.628880.52199.14
2.14-2.1712.871.5021.928390.433100
2.17-2.2213.281.182.528680.335100
2.22-2.2613.810.9873.129000.274100
2.26-2.3113.610.7863.828490.2299.93
2.31-2.3613.540.6144.829040.172100
2.36-2.4213.170.5095.828960.14599.97
2.42-2.4912.830.3887.228670.112100
2.49-2.5613.710.319.228670.087100
2.56-2.6413.650.23512.229100.066100
2.64-2.7413.120.17515.429080.05100
2.74-2.8513.430.14518.929010.041100
2.85-2.9813.830.11423.829210.032100
2.98-3.1413.530.0832.728900.02399.97
3.14-3.3312.790.06339.829210.018100
3.33-3.5913.360.04456.829620.013100
3.59-3.9512.470.03570.229220.01100
3.95-4.5213.030.0288529840.008100
4.52-5.6912.350.02588.730060.007100
5.69-5011.980.0296.731470.006100

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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: 5Y0N

5y0n


Resolution: 2.1→48.967 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.96
RfactorNum. reflection% reflection
Rfree0.2428 2919 5 %
Rwork0.2015 --
obs0.2046 58350 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 176.67 Å2 / Biso mean: 62.55 Å2 / Biso min: 29.34 Å2
Refinement stepCycle: final / Resolution: 2.1→48.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6410 0 62 67 6539
Biso mean--72.42 45.5 -
Num. residues----802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076614
X-RAY DIFFRACTIONf_angle_d1.1868948
X-RAY DIFFRACTIONf_chiral_restr0.044992
X-RAY DIFFRACTIONf_plane_restr0.0051124
X-RAY DIFFRACTIONf_dihedral_angle_d16.6772480
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 95 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0993-2.13550.36291460.361727612907
2.1355-2.17440.35291420.351526952837
2.1744-2.21620.35531430.333427282871
2.2162-2.26140.35531450.334627532898
2.2614-2.31060.37711430.325927082851
2.3106-2.36430.35191440.307627432887
2.3643-2.42350.33931450.293627622907
2.4235-2.4890.36531440.301127192863
2.489-2.56220.31271430.296727212864
2.5622-2.64490.32771460.270827752921
2.6449-2.73940.351450.267127522897
2.7394-2.84910.31521450.265627552900
2.8491-2.97880.29661450.263527712916
2.9788-3.13580.30251450.248227412886
3.1358-3.33220.30651460.236127792925
3.3322-3.58940.24931480.206128112959
3.5894-3.95050.23581460.183227742920
3.9505-4.52180.15871490.147428322981
4.5218-5.69560.17561500.140128563006
5.6956-48.97380.19141580.141329883146
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)
12.4182-0.39491.46380.894-0.25222.53710.00380.23560.003-0.5705-0.1232-0.0073-0.8587-0.50850.07470.77370.1974-0.00640.6441-0.03370.212117.8167-7.7767-56.9364
28.24142.21615.8734.01863.61139.48050.37460.7648-0.4707-0.33480.2032-0.63592.18990.4621-0.55821.03630.0079-0.00190.59330.10750.349345.6769-2.8603-63.3505
31.18810.24570.30041.39660.81654.5003-0.01270.05920.057-0.3781-0.0140.0543-0.9637-0.38020.04770.57340.10280.03020.51820.02270.231620.527-5.9177-45.3687
40.9952-0.3838-0.53581.39580.28932.5499-0.1644-0.574-0.02830.3216-0.02010.1244-0.5903-0.97290.15670.55840.1694-0.01590.8395-0.01120.247724.567-0.98153.9591
52.34.31592.40738.50154.00145.77460.6072-0.1757-0.43840.5055-0.0962-0.81450.51550.8168-0.46820.45560.1783-0.02850.80990.02350.433119.7184-29.204510.5039
61.29130.2080.36381.62020.2513.2616-0.0605-0.22370.06070.0560.03210.081-0.3319-0.69890.0410.40090.07160.00240.60020.01710.22522.6593-3.9132-7.4344
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:105)A1 - 105
2X-RAY DIFFRACTION2(chain A and resid 106:153)A106 - 153
3X-RAY DIFFRACTION3(chain A and resid 154:414)A154 - 414
4X-RAY DIFFRACTION4(chain B and resid 1:105)B1 - 105
5X-RAY DIFFRACTION5(chain B and resid 106:153)B106 - 153
6X-RAY DIFFRACTION6(chain B and resid 154:414)B154 - 414

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