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- PDB-6bqy: Crystal Structure of Tyrosine-tRNA Synthetase from Acinetobacter ... -

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Basic information

Entry
Database: PDB / ID: 6bqy
TitleCrystal Structure of Tyrosine-tRNA Synthetase from Acinetobacter baumannii
ComponentsTyrosine--tRNA ligase
KeywordsLIGASE / SSGCID / Tyrosine--tRNA ligase / Acinetobacter baumannii / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / RNA binding / ATP binding / metal ion binding / cytosol
Similarity search - Function
Tyrosine-tRNA ligase, bacterial-type, type 2 / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / S4 RNA-binding domain profile. ...Tyrosine-tRNA ligase, bacterial-type, type 2 / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / S4 RNA-binding domain profile. / RNA-binding S4 domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Tyrosine--tRNA ligase / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal Structure of Glutamate-tRNA Synthetase from Helicobacter pylori
Authors: Dranow, D.M. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionNov 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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: Tyrosine--tRNA ligase
B: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0279
Polymers90,5932
Non-polymers4347
Water54030
1
A: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4824
Polymers45,2961
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5455
Polymers45,2961
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.370, 56.620, 64.070
Angle α, β, γ (deg.)87.950, 113.850, 109.520
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Tyrosine--tRNA ligase / Tyrosyl-tRNA synthetase / TyrRS


Mass: 45296.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: tyrS, A7A59_01455, A7A65_06465, A7M79_16285, A7M90_19385, A7N09_15205, APD06_07635, APD31_16655, B9X91_04915, B9X95_11600, BGC29_18795, BWP00_10095, CAS83_08605, CBI29_00001, IX87_14380, LV38_03496
Plasmid: AcbaC.01032.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A086HYS2, UniProt: B0VML7*PLUS, tyrosine-tRNA ligase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 1.83 Å3/Da / Density % sol: 32.79 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20.0 mg/mL AcbaC.01032.a.B2.PW38226, 1:1 with MCSG1(g1) (0.1 M HEPES:NaOH, pH 7.5, 10% w/v PEG8000, 8% v/v ethylene glycol), cryoprotectant: 20% ethylene glycol, Tray: 291063g1, puck: ikf2-10

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 11, 2017 / Details: Beryllium Lenses
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.1→31.159 Å / Num. obs: 36717 / % possible obs: 97.8 % / Redundancy: 3.918 % / Biso Wilson estimate: 42.08 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.055 / Χ2: 1.027 / Net I/σ(I): 12.85 / Num. measured all: 143863 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.153.9830.5992.3526680.9390.69296.7
2.15-2.213.9830.4592.926180.9630.5396.7
2.21-2.283.9760.3943.3225640.9730.45696.9
2.28-2.353.9790.284.3224820.9830.32497.4
2.35-2.423.9780.2145.2224170.990.24797.5
2.42-2.513.9770.1776.2923160.9910.20597.1
2.51-2.63.9650.1357.6722570.9950.15697.7
2.6-2.713.9590.1298.2521970.9940.14997.8
2.71-2.833.9550.09210.2820900.9970.10697.9
2.83-2.973.950.07212.7420050.9970.08398
2.97-3.133.9240.06114.9319220.9970.07198.5
3.13-3.323.9070.0518.2918000.9980.05898.4
3.32-3.553.8590.04321.8217210.9980.04998.6
3.55-3.833.8280.03725.1215680.9980.04398.9
3.83-4.23.8230.03628.3614450.9980.04298.8
4.2-4.73.820.03331.4313360.9980.03998.6
4.7-5.423.770.03432.1911690.9980.03999.1
5.42-6.643.70.03531.99780.9980.0499
6.64-9.393.6840.03333.257710.9980.03898.7
9.39-31.1593.4910.03132.83930.9980.03794.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HSE

1hse


Resolution: 2.1→31.159 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 38.14
RfactorNum. reflection% reflection
Rfree0.226 1694 5.42 %
Rwork0.188 --
obs0.1901 31272 83.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 153.89 Å2 / Biso mean: 72.4682 Å2 / Biso min: 40.38 Å2
Refinement stepCycle: final / Resolution: 2.1→31.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 0 28 30 3430
Biso mean--80.58 64.85 -
Num. residues----434
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1001-2.16190.36581160.34851960207667
2.1619-2.23160.38471090.30552015212468
2.2316-2.31140.3881170.29462149226673
2.3114-2.40390.33431290.24822169229874
2.4039-2.51330.29311340.23572279241377
2.5133-2.64570.2651330.21252375250880
2.6457-2.81140.25771420.2272465260783
2.8114-3.02830.27291530.22452648280190
3.0283-3.33270.27271580.22042824298295
3.3327-3.81420.22171670.1872875304298
3.8142-4.80270.1711670.15282885305299
4.8027-31.1620.18931690.14932934310399
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)
15.0823-0.691-0.38672.13822.75818.6890.0513-0.27080.32080.3356-0.06530.14570.0625-0.06090.06660.4823-0.05530.06570.3099-0.05140.551142.293229.4747-18.0225
23.6354-3.2313-2.24383.85542.99244.5046-0.2532-0.55330.05990.91250.05080.26350.580.33720.13480.5085-0.03710.04660.54690.00170.473654.467218.2881-18.0922
34.6223-0.0736-0.83618.51154.90093.70710.01730.3327-0.25870.09330.1415-0.24680.30330.231-0.16020.45970.00610.00110.6039-0.01550.326933.056754.565613.4238
44.8369-1.1311-3.10954.3682.66246.1486-0.1960.3435-0.60770.33210.04540.19490.7940.08270.15790.4387-0.02650.02490.4395-0.04580.567721.024851.814323.6296
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 137 )A9 - 137
2X-RAY DIFFRACTION2chain 'A' and (resid 138 through 227 )A138 - 227
3X-RAY DIFFRACTION3chain 'B' and (resid 9 through 137 )B9 - 137
4X-RAY DIFFRACTION4chain 'B' and (resid 138 through 227 )B138 - 227

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