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

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Basic information

Entry
Database: PDB / ID: 6bqz
TitleCrystal Structure of Tyrosine-tRNA Synthetase from Acinetobacter baumannii with bound L-Tyrosine
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 / cytoplasm
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 / RNA-binding S4 domain superfamily ...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 / RNA-binding S4 domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / TYROSINE / Tyrosine--tRNA ligase / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal Structure of Tyrosine-tRNA Synthetase from Acinetobacter baumannii with bound L-Tyrosine
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 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)91,0637
Polymers90,5932
Non-polymers4705
Water2,090116
1
A: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5023
Polymers45,2961
Non-polymers2052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5614
Polymers45,2961
Non-polymers2653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.260, 49.800, 73.370
Angle α, β, γ (deg.)87.650, 107.110, 113.860
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-TYR / TYROSINE / Tyrosine


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 1.69 Å3/Da / Density % sol: 27.41 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20.0 mg/mL AcbaC.01032.a.B2.PW38226 in 3 mM L-Tyr, magnesium chloride, AMPPNP, 1:1 with MCSG1(b7) (0.17 M ammonium acetate, 0.085 M sodium citrate:HCl, pH 5.6, 25.5% w/v PEG4000, 15% v/v ...Details: 20.0 mg/mL AcbaC.01032.a.B2.PW38226 in 3 mM L-Tyr, magnesium chloride, AMPPNP, 1:1 with MCSG1(b7) (0.17 M ammonium acetate, 0.085 M sodium citrate:HCl, pH 5.6, 25.5% w/v PEG4000, 15% v/v glycerol), Tray: 291066b7, puck: ikf2-3

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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: 2.3→29.624 Å / Num. obs: 25961 / % possible obs: 98.2 % / Redundancy: 3.904 % / Biso Wilson estimate: 37.71 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.085 / Χ2: 1.029 / Net I/σ(I): 11.87 / Num. measured all: 101357 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.363.9710.5592.937486194218850.9270.64697.1
2.36-2.423.9710.4063.767425192618700.9570.4797.1
2.42-2.493.9720.3394.337137183417970.9690.39298
2.49-2.573.9790.2595.417007181017610.9760.397.3
2.57-2.663.9650.2296.026769173717070.9780.26598.3
2.66-2.753.9630.1946.86607169316670.9820.22598.5
2.75-2.853.9510.1498.366354164316080.9880.17297.9
2.85-2.973.9580.1239.946055155715300.9910.14298.3
2.97-3.13.9250.10411.65786149014740.9920.1298.9
3.1-3.253.8990.08214.155533144414190.9930.09698.3
3.25-3.433.8790.06816.015194136313390.9950.07998.2
3.43-3.643.8380.06717.094951130412900.9940.07898.9
3.64-3.893.7550.05718.84487120911950.9950.06798.8
3.89-4.23.8270.05121.44236112111070.9930.05998.8
4.2-4.63.8380.04523.23988105210390.9970.05398.8
4.6-5.143.7970.04623.1735209339270.9960.05499.4
5.14-5.943.8090.04523.2331588438290.9960.05398.3
5.94-7.273.750.04922.7726067016950.9950.05799.1
7.27-10.293.7660.0424.9720115405340.9960.04798.9
10.29-29.6243.6350.03925.2910472972880.9970.04697

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6BQZ

6bqz


Resolution: 2.3→29.624 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 28.66
RfactorNum. reflection% reflection
Rfree0.2307 1987 7.67 %
Rwork0.1804 --
obs0.1844 25900 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 117.97 Å2 / Biso mean: 51.8793 Å2 / Biso min: 25.96 Å2
Refinement stepCycle: final / Resolution: 2.3→29.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3369 0 32 117 3518
Biso mean--62.48 50.27 -
Num. residues----430
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.35760.27891320.22431685181797
2.3576-2.42130.28531340.21781705183997
2.4213-2.49250.29491290.2151696182597
2.4925-2.57290.25691350.2151695183097
2.5729-2.66480.28891340.21681711184598
2.6648-2.77140.29741550.22091715187098
2.7714-2.89740.27351470.21161684183198
2.8974-3.05010.31371580.21191699185798
3.0501-3.24090.25851340.20951715184999
3.2409-3.49080.23041340.1911741187599
3.4908-3.84140.20291320.1711741187399
3.8414-4.39580.20081540.15261703185799
4.3958-5.53230.19711580.14661719187799
5.5323-29.6260.18871510.1561704185599
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)
13.40721.17140.92135.15610.52873.8647-0.1144-0.05590.0820.6333-0.2881-0.471-0.230.44210.38720.6608-0.0826-0.14880.53390.1140.32827.514449.633527.7202
23.28340.22221.92943.0601-2.12194.69230.0912-0.0773-0.27170.08270.18970.26030.552-0.1852-0.25920.5273-0.108-0.00640.38060.01930.257-9.093753.015512.4888
31.2542-0.0514-0.23862.0879-1.5284.13590.0546-0.1374-0.02980.3513-0.1677-0.16250.15520.47460.1220.4065-0.0516-0.05990.39680.07390.35646.10159.37925.9624
42.15592.7445-0.62063.79930.10092.78140.350.8389-0.69640.9375-0.5570.40771.98841.22590.00650.7169-0.08110.13270.8502-0.30850.4202-2.03354.59577.0956
54.76491.50190.64794.7952-1.54528.5809-0.18270.2340.0352-1.04620.04540.28840.6601-0.28430.14280.6581-0.0436-0.05470.46330.06720.26550.790932.420936.1647
60.9650.4588-0.93614.2639-1.97243.46930.03970.15210.079-0.2001-0.0237-0.1163-0.34950.49640.07890.4773-0.071-0.07920.43150.10940.35142.851638.376251.8966
72.73270.58380.27022.81660.58395.49110.1325-0.10860.03110.6719-0.2554-0.1905-0.66040.46760.22990.4941-0.0826-0.10370.29540.05770.29461.3139.296664.0887
88.8368-2.3662-2.53224.49991.51324.25210.12850.44260.2906-0.2012-0.015-0.39790.04590.431-0.14840.3719-0.0622-0.00690.31320.0970.30668.658815.856161.5868
91.6253-0.3893-0.19244.6041-3.35077.9444-0.0773-0.0516-0.1468-0.48280.02050.02630.6558-0.24680.08140.4998-0.0154-0.02140.26910.04110.30882.422725.095753.2746
109.13416.44555.17434.59633.50643.3646-0.98121.51489.6096-0.66380.64871.84970.2242.80370.12730.40750.0825-0.15980.9376-0.00630.8535.765730.828258.4786
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 39 )A8 - 39
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 137 )A40 - 137
3X-RAY DIFFRACTION3chain 'A' and (resid 138 through 227 )A138 - 227
4X-RAY DIFFRACTION4chain 'A' and (resid 400 through 400 )A400
5X-RAY DIFFRACTION5chain 'B' and (resid 9 through 39 )B9 - 39
6X-RAY DIFFRACTION6chain 'B' and (resid 40 through 86 )B40 - 86
7X-RAY DIFFRACTION7chain 'B' and (resid 87 through 137 )B87 - 137
8X-RAY DIFFRACTION8chain 'B' and (resid 138 through 172 )B138 - 172
9X-RAY DIFFRACTION9chain 'B' and (resid 173 through 227 )B173 - 227
10X-RAY DIFFRACTION10chain 'B' and (resid 400 through 400 )B400

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