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- PDB-6otj: Crystal Structure of Tyrosyl-tRNA synthetase from Neisseria gonor... -

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Basic information

Entry
Database: PDB / ID: 6otj
TitleCrystal Structure of Tyrosyl-tRNA synthetase from Neisseria gonorrhoeae with bound L-Tyr
ComponentsTyrosine--tRNA ligase
KeywordsLIGASE / SSGCID / aminoacylation / tRNA binding / 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 1 / 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. / Rossmann-like alpha/beta/alpha sandwich fold / RNA-binding S4 domain / RNA-binding S4 domain superfamily / S4 RNA-binding domain profile.
Similarity search - Domain/homology
TYROSINE / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Tyrosyl-tRNA synthetase from Neisseria gonorrhoeae with bound L-Tyr
Authors: Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionMay 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

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Assembly

Deposited unit
A: Tyrosine--tRNA ligase
B: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,79552
Polymers96,5352
Non-polymers4,26050
Water93752
1
A: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,64028
Polymers48,2681
Non-polymers2,37327
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,15424
Polymers48,2681
Non-polymers1,88723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.730, 121.730, 301.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 48267.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (strain NCCP11945) (bacteria)
Strain: NCCP11945 / Gene: tyrS, NGK_0091 / Plasmid: NegoA.01032.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B4RP13, tyrosine-tRNA ligase
#2: Chemical ChemComp-TYR / TYROSINE / Tyrosine


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C9H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: SO4
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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

Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: NegoA.01032.a.B1.PW37921 at 26 mg/ml was incubated with 4 mM L-Tyr, then was mixed 1:1 with NegoTyrRSv1(d3): 270 mM HEPES free acid/ NaOH, pH = 7.6, 1700 mM ammonium sulfate, cryo: 20% ...Details: NegoA.01032.a.B1.PW37921 at 26 mg/ml was incubated with 4 mM L-Tyr, then was mixed 1:1 with NegoTyrRSv1(d3): 270 mM HEPES free acid/ NaOH, pH = 7.6, 1700 mM ammonium sulfate, cryo: 20% ethylene glycol. Tray: 301932d3, puck: nky3-3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 5, 2018 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.85→47.879 Å / Num. obs: 52573 / % possible obs: 97.5 % / Redundancy: 4.183 % / Biso Wilson estimate: 63.489 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.078 / Χ2: 1.023 / Net I/σ(I): 15.99 / Num. measured all: 219900 / Scaling rejects: 24
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
2.85-2.924.1690.5812.4116340393039190.8850.66999.7
2.92-34.1680.492.8515785380037870.9120.56399.7
3-3.094.1610.3853.5515401370937010.9330.44399.8
3.09-3.194.1630.3054.5815109364036290.9510.35199.7
3.19-3.294.1430.2086.2314514351735030.9770.23999.6
3.29-3.414.1580.1667.7213974337533610.9850.1999.6
3.41-3.534.1640.1299.5713588328232630.9920.14799.4
3.53-3.684.1530.09512.5513069318631470.9950.10898.8
3.68-3.844.1910.08114.9912530303029900.9950.09398.7
3.84-4.034.1750.06817.7811883290828460.9970.07797.9
4.03-4.254.2020.0522.0511446278627240.9980.05797.8
4.25-4.514.1810.0426.3910815265825870.9990.04697.3
4.51-4.824.2040.0428.3610059247623930.9990.04596.6
4.82-5.24.2290.0428.639430232922300.9980.04595.7
5.2-5.74.2510.03929.328673215720400.9980.04494.6
5.7-6.374.2610.03631.037875197718480.9990.04193.5
6.37-7.364.30.03135.696858173815950.9990.03691.8
7.36-9.014.2940.02443.865849151313620.9990.02790
9.01-12.754.1880.02250.724423119710560.9990.02588.2
12.75-47.8793.850.02249.7322797275920.9990.02681.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472)refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OUD

4oud


Resolution: 2.85→47.879 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.9
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 1946 3.71 %RANDOM, 0
Rwork0.1962 ---
obs0.1973 52488 97.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 203.93 Å2 / Biso mean: 78.9373 Å2 / Biso min: 22.14 Å2
Refinement stepCycle: final / Resolution: 2.85→47.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6489 0 245 54 6788
Biso mean--128.63 59.31 -
Num. residues----858
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 (%)
2.85-2.92130.39181320.35943617374999
2.9213-3.00030.3721410.32553589373099
3.0003-3.08850.29821240.295236443768100
3.0885-3.18820.29051350.268936623797100
3.1882-3.30210.27351490.25633627377699
3.3021-3.43430.27941590.24373616377599
3.4343-3.59060.26251410.23213644378599
3.5906-3.77980.22751300.19123625375599
3.7798-4.01650.22151520.17633608376098
4.0165-4.32640.18841360.15023627376398
4.3264-4.76140.16671460.13753588373497
4.7614-5.44960.17791250.16133592371795
5.4496-6.86270.23251330.18743558369193
6.8627-47.88560.19251430.17583545368889
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)
11.6708-0.91510.0870.4573-0.253.5305-0.2638-0.07190.0361-0.12170.0017-0.07180.20110.35860.23270.57660.06450.05230.22780.04050.444-45.6691-23.3128-12.7618
21.8213-0.24990.40390.0981-0.3363.6224-0.2702-0.06840.00510.08560.0498-0.04830.1678-0.02280.18310.61650.01740.06660.21490.02760.446-53.1372-22.1272-24.0596
31.69090.49430.2691.2529-1.04044.6197-0.3234-0.0662-0.157-0.1481-0.007-0.1430.65560.33510.33060.53980.07230.05350.22960.03150.4389-48.4248-27.3921-13.6988
43.3704-0.7574-0.25281.19590.44031.4494-0.1837-0.6602-0.03420.24660.117-0.01270.3076-0.15460.04160.6110.18080.02130.4374-0.00240.4427-53.9604-24.620611.6131
54.26873.7359-4.10823.9407-2.33796.307-0.5373-0.1311-1.24640.1337-0.20960.41631.0301-0.55580.75491.0507-0.21940.26110.8481-0.01541.142-83.5854-33.274521.9065
67.20291.4525-2.24881.7572-0.21133.44310.0067-0.636-0.9692-0.2511-0.5315-0.01280.6504-0.06480.36830.6720.04020.16830.7348-0.01850.5937-78.8198-24.69324.4298
75.15465.85261.9998221.99980.61610.13020.15560.23-0.1591-0.0897-1.0816-0.11-0.33620.48620.10480.00660.6296-0.57341.4469-52.3372-23.873-18.5117
82.4616-0.65410.21321.04970.04463.91990.05520.3110.3395-0.3486-0.23360.0879-0.9197-0.53040.13550.58950.209-0.0210.7031-0.01150.4053-87.60668.324517.6882
91.3288-0.51370.27230.5855-0.71544.5343-0.04780.08780.0488-0.0344-0.09630.1474-0.7889-0.95750.15780.45560.1779-0.01840.7579-0.06640.43-92.66013.344227.6173
100.9087-0.2786-0.73531.80970.53530.96120.22920.6297-0.1192-0.8062-0.31140.2477-0.6397-0.97580.04720.84330.3669-0.03711.2345-0.03350.5115-91.0448-1.1533-6.2326
111.44871.33843.27258.28215.86058.7879-0.57730.529-0.5598-0.3475-0.13160.70982.3142-1.19630.52131.3002-0.51550.31971.172-0.16960.7462-87.7102-32.5263-14.6583
122.75921.91912.39519.4893.82815.0659-0.22880.3713-0.6781-0.6380.05920.27430.1125-0.80970.30060.7417-0.10480.17581.1393-0.20070.5822-82.0282-24.7606-18.016
131.99992.00012.000121.99991.9999-0.66074.25771.5955-0.22410.6092.7967-0.23863.57910.06260.49080.15180.13951.21230.40771.332-88.86752.813923.582
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 90 )A1 - 90
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 186 )A91 - 186
3X-RAY DIFFRACTION3chain 'A' and (resid 187 through 248 )A187 - 248
4X-RAY DIFFRACTION4chain 'A' and (resid 249 through 349 )A249 - 349
5X-RAY DIFFRACTION5chain 'A' and (resid 350 through 376 )A350 - 376
6X-RAY DIFFRACTION6chain 'A' and (resid 377 through 431 )A377 - 431
7X-RAY DIFFRACTION7chain 'A' and (resid 501 through 501 )A501
8X-RAY DIFFRACTION8chain 'B' and (resid -3 through 128 )B-3 - 128
9X-RAY DIFFRACTION9chain 'B' and (resid 129 through 248 )B129 - 248
10X-RAY DIFFRACTION10chain 'B' and (resid 249 through 349 )B249 - 349
11X-RAY DIFFRACTION11chain 'B' and (resid 350 through 376 )B350 - 376
12X-RAY DIFFRACTION12chain 'B' and (resid 377 through 431 )B377 - 431
13X-RAY DIFFRACTION13chain 'B' and (resid 501 through 501 )B501

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