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- PDB-9o66: Crystal Structure of Tryptophanyl-tRNA synthetase from Klebsiella... -

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Basic information

Entry
Database: PDB / ID: 9o66
TitleCrystal Structure of Tryptophanyl-tRNA synthetase from Klebsiella aerogenes
ComponentsTryptophan--tRNA ligase
KeywordsLIGASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Tryptophanyl-tRNA synthetase / Klebsiella aerogenes
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophanyl-tRNA aminoacylation / tryptophan-tRNA ligase activity / ATP binding / cytosol
Similarity search - Function
Tryptophan-tRNA ligase, bacterial-type / : / Tryptophan-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
Similarity search - Domain/homology
IMIDAZOLE / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesKlebsiella aerogenes KCTC 2190 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of Tryptophanyl-tRNA synthetase from Klebsiella aerogenes
Authors: Seibold, S. / Lovell, S. / Battaile, K.P.
History
DepositionApr 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,7115
Polymers79,5322
Non-polymers1783
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-33 kcal/mol
Surface area26780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.156, 75.510, 56.754
Angle α, β, γ (deg.)90.00, 95.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Tryptophan--tRNA ligase / Tryptophanyl-tRNA synthetase / TrpRS


Mass: 39766.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes KCTC 2190 (bacteria)
Gene: trpS, EAE_05135 / Plasmid: KlaeA.00241.a.UX1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3FKK2, tryptophan-tRNA ligase
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.05 Å3/Da / Density % sol: 40.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus A1: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Imidazole/MES, pH 6.5, 30 mM MgCl2 and 30 mM CaCl2. KlaeA.00241.a.UX1.PW39324 at 11.1 mg/mL. plate 19612 A1 drop 1. Puck: PSL-1906, Cryo: Direct

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 15, 2024
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.1→47.77 Å / Num. obs: 37570 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.978 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.073 / Rrim(I) all: 0.188 / Χ2: 1.06 / Net I/σ(I): 8.8 / Num. measured all: 251613
Reflection shellResolution: 2.1→2.16 Å / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 1.098 / Num. measured all: 20511 / Num. unique obs: 3047 / CC1/2: 0.618 / Rpim(I) all: 0.456 / Rrim(I) all: 1.191 / Χ2: 0.99 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
PHENIXdev_5660refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→43.27 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.247 1840 4.9 %
Rwork0.2014 --
obs0.2036 37529 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→43.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4807 0 11 169 4987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034937
X-RAY DIFFRACTIONf_angle_d0.5446705
X-RAY DIFFRACTIONf_dihedral_angle_d17.0731782
X-RAY DIFFRACTIONf_chiral_restr0.041757
X-RAY DIFFRACTIONf_plane_restr0.004880
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.31281450.26912715X-RAY DIFFRACTION100
2.16-2.220.29051550.25542705X-RAY DIFFRACTION100
2.22-2.290.31931360.28352712X-RAY DIFFRACTION98
2.29-2.370.28081340.22892746X-RAY DIFFRACTION100
2.37-2.470.27951390.21682747X-RAY DIFFRACTION100
2.47-2.580.24261390.21192752X-RAY DIFFRACTION100
2.58-2.720.22341410.20032706X-RAY DIFFRACTION100
2.72-2.890.24941600.19482731X-RAY DIFFRACTION100
2.89-3.110.26561480.2032748X-RAY DIFFRACTION100
3.11-3.420.26681210.19682785X-RAY DIFFRACTION100
3.42-3.920.20561320.18392757X-RAY DIFFRACTION99
3.92-4.930.21141460.1622754X-RAY DIFFRACTION99
4.94-43.270.23821440.19632831X-RAY DIFFRACTION100
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)
11.7379-0.5163-1.422.2525-0.66711.7242-0.2602-0.59430.49060.8907-0.08460.2393-0.27390.12380.3360.4597-0.03910.05340.3749-0.03420.383916.671-0.570725.4032
20.90470.1256-0.18551.2301-0.11811.15470.0138-0.10590.0170.1793-0.02250.2133-0.0377-0.09290.01170.2387-0.00150.01170.1652-0.0120.183225.50752.156917.7948
30.61120.3377-0.460.31510.06623.66360.16-0.09060.07580.4533-0.00970.15020.18-0.8152-0.09480.57110.0054-0.00510.3763-0.00970.404916.77849.512625.41
41.9162-0.71461.10942.4092.11083.63290.2782-0.1685-0.1297-0.1934-0.3363-0.1260.3255-0.33230.11930.6207-0.07450.09040.6103-0.080.632817.4098-1.224243.8968
50.9212-0.2230.34860.98930.37581.08710.043-0.38380.43280.139-0.46520.6709-0.0628-0.60440.38420.494-0.12290.12390.7079-0.27270.87394.34251.484242.6794
60.97660.7366-1.27350.9209-1.09862.3153-0.08060.004-0.16770.0384-0.0170.07160.456-0.12210.06030.3472-0.0705-0.00560.1943-0.01510.257526.7789-8.34966.9259
72.2418-0.0032-0.93570.0710.29431.60960.064-0.07680.3438-0.3218-0.0715-0.4464-0.04630.311-0.00440.2827-0.00270.01350.32010.04380.292157.9055-3.0469-2.1337
80.4778-0.1784-0.57040.90980.74441.3241-0.0141-0.06350.01620.03210.0192-0.08310.00320.1525-0.00710.212-0.0168-0.02460.19230.00320.147348.0085-1.42242.3103
91.731-1.4739-0.10753.0280.29781.15560.1199-0.16170.2105-0.26860.0231-0.2501-0.04650.4062-0.16890.2442-0.0392-0.01840.2439-0.02050.14550.1313-0.917110.6627
103.35880.6265-0.6333.6957-0.89073.2066-0.17080.12790.5615-0.10220.0611-0.4935-0.19490.48440.07830.2775-0.0528-0.07060.3126-0.02290.279653.8412-0.414418.4901
111.91790.968-2.23471.5587-1.83353.0641-0.2582-0.26980.0242-0.1416-0.0542-0.37040.03320.6050.32310.245-0.1241-0.09930.4445-0.01580.346162.6452-1.37626.2484
122.06871.08680.17493.06470.33450.9254-0.0749-0.33551.2050.0018-0.20780.2866-0.50010.01770.29450.3966-0.05460.0070.57750.07430.835961.93710.5163-10.4648
131.56170.349-0.83841.224-0.01350.6632-0.08040.1724-0.0082-0.3298-0.1033-0.88390.02480.59510.13620.3972-0.02910.04710.71180.18960.720670.93754.1061-17.7302
140.5549-0.2987-0.56760.96780.3822.77630.049-0.0607-0.06910.163-0.04280.08750.09260.1455-0.01980.2176-0.0135-0.03510.12170.01020.185340.4439-12.80426.3909
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 168 )
3X-RAY DIFFRACTION3chain 'A' and (resid 169 through 195 )
4X-RAY DIFFRACTION4chain 'A' and (resid 196 through 221 )
5X-RAY DIFFRACTION5chain 'A' and (resid 222 through 298 )
6X-RAY DIFFRACTION6chain 'A' and (resid 299 through 334 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 24 )
8X-RAY DIFFRACTION8chain 'B' and (resid 25 through 122 )
9X-RAY DIFFRACTION9chain 'B' and (resid 123 through 147 )
10X-RAY DIFFRACTION10chain 'B' and (resid 148 through 168 )
11X-RAY DIFFRACTION11chain 'B' and (resid 169 through 191 )
12X-RAY DIFFRACTION12chain 'B' and (resid 192 through 212 )
13X-RAY DIFFRACTION13chain 'B' and (resid 213 through 298 )
14X-RAY DIFFRACTION14chain 'B' and (resid 299 through 334 )

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