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- PDB-6aqh: Crystal Structure of Lysyl-tRNA Synthetase from Mycobacterium the... -

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Basic information

Entry
Database: PDB / ID: 6aqh
TitleCrystal Structure of Lysyl-tRNA Synthetase from Mycobacterium thermoresistibile complexed with L-lysine and Cladosporin
ComponentsLysine--tRNA ligase
KeywordsLIGASE/INHIBITOR / SSGCID / Lysine--tRNA ligase / synthetase / cladosporin / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / LIGASE-INHIBITOR complex
Function / homology
Function and homology information


lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / nucleic acid binding / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II ...Lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
cladosporin / LYSINE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesMycobacterium thermoresistibile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Lysyl-tRNA Synthetase from Mycobacterium thermoresistibile complexed with L-lysine and Cladosporin
Authors: Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionAug 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 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: Lysine--tRNA ligase
B: Lysine--tRNA ligase
C: Lysine--tRNA ligase
D: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,83614
Polymers227,9544
Non-polymers1,88210
Water4,900272
1
A: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4283
Polymers56,9881
Non-polymers4402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5525
Polymers56,9881
Non-polymers5644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4283
Polymers56,9881
Non-polymers4402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4283
Polymers56,9881
Non-polymers4402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Lysine--tRNA ligase
C: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,8566
Polymers113,9772
Non-polymers8794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8470 Å2
ΔGint-39 kcal/mol
Surface area37590 Å2
MethodPISA
6
B: Lysine--tRNA ligase
D: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,9808
Polymers113,9772
Non-polymers1,0036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9050 Å2
ΔGint-32 kcal/mol
Surface area37790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.460, 88.160, 123.430
Angle α, β, γ (deg.)93.340, 96.450, 98.930
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Lysine--tRNA ligase / Lysyl-tRNA synthetase / LysRS


Mass: 56988.488 Da / Num. of mol.: 4 / Fragment: MyulA.00612.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium thermoresistibile (strain ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316) (bacteria)
Strain: ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316
Gene: lysS, KEK_07907 / Plasmid: MythA.00612.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G7CF12, lysine-tRNA ligase
#2: Chemical
ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical
ChemComp-KRS / cladosporin / (3R)-3-[[(2R,6S)-6-methyloxan-2-yl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one


Mass: 292.327 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H20O5
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.5 Å3/Da / Density % sol: 50.75 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9.1
Details: MythA.00612.a.B1.PW38257 at 33.5 mg/ml was incubated with 2 mM L-Lysine and 1 mM cladosporin, then mixed 1:1 with MCSG1 (d12): 0.2 M ammonium chloride, pH = 6.3, 20% (w/v) PEG-3350, ...Details: MythA.00612.a.B1.PW38257 at 33.5 mg/ml was incubated with 2 mM L-Lysine and 1 mM cladosporin, then mixed 1:1 with MCSG1 (d12): 0.2 M ammonium chloride, pH = 6.3, 20% (w/v) PEG-3350, cryoprotected with 20% ethylene glycol. Tray: 293203d12, puck: ryc9-9.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 4, 2017 / 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: 2.35→42.457 Å / Num. obs: 87176 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Redundancy: 2.285 % / Biso Wilson estimate: 47.06 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.072 / Χ2: 1 / Net I/σ(I): 10.13 / Num. measured all: 199158 / Scaling rejects: 53
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
2.35-2.412.3780.5761.9715504683165210.8660.75195.5
2.41-2.482.3770.4842.3114900659762680.8910.6395
2.48-2.552.3640.3832.9214657651662000.9220.49895.2
2.55-2.632.3640.3043.5714010622059260.9540.39595.3
2.63-2.712.3510.2454.1913402602357000.9680.3294.6
2.71-2.812.3450.1875.2513143594656040.9810.24494.2
2.81-2.912.3180.1486.6412261560752890.9840.19494.3
2.91-3.032.3020.1187.8611859546851510.9880.15594.2
3.03-3.172.2710.0869.911179524349220.9910.11493.9
3.17-3.322.2460.0681210495498346720.9930.09193.8
3.32-3.52.2180.05414.199796473744170.9940.07393.2
3.5-3.722.1880.04416.49158448741860.9950.0693.3
3.72-3.972.1810.03917.648699423039880.9960.05394.3
3.97-4.292.1640.03519.358055391537220.9960.04795.1
4.29-4.72.1610.03220.727441360534430.9970.04395.5
4.7-5.252.170.03320.86873329431680.9970.04496.2
5.25-6.072.1980.03320.46146288627960.9960.04496.9
6.07-7.432.2150.03121.325284243423860.9970.0498
7.43-10.512.240.03222.594138187718470.9970.04198.4
10.51-42.4572.2250.02922.91215810259700.9970.03794.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VL1

5vl1


Resolution: 2.35→42.457 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 32.14
RfactorNum. reflection% reflection
Rfree0.2538 2073 2.38 %
Rwork0.2243 --
obs0.225 86921 94.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 129.92 Å2 / Biso mean: 59.27 Å2 / Biso min: 29.89 Å2
Refinement stepCycle: final / Resolution: 2.35→42.457 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14952 0 132 273 15357
Biso mean--51.84 47.5 -
Num. residues----1953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215441
X-RAY DIFFRACTIONf_angle_d0.43721035
X-RAY DIFFRACTIONf_chiral_restr0.042389
X-RAY DIFFRACTIONf_plane_restr0.0042765
X-RAY DIFFRACTIONf_dihedral_angle_d14.7249235
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.40470.37731250.33785723584895
2.4047-2.46480.38311280.33765633576195
2.4648-2.53140.36351300.32725708583895
2.5314-2.60590.41381420.32255636577895
2.6059-2.690.32061680.31445656582494
2.69-2.78610.36221390.30675582572194
2.7861-2.89770.35011560.29745622577894
2.8977-3.02950.31311400.29935575571594
3.0295-3.18920.33661200.29145646576694
3.1892-3.38890.28211520.2655575572794
3.3889-3.65040.25151310.23815584571593
3.6504-4.01750.23031340.20735638577294
4.0175-4.59830.18791280.16235713584195
4.5983-5.7910.19061350.16855741587696
5.791-42.46350.17871450.15465816596197
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)
12.10720.1201-0.27212.4027-0.24713.2697-0.22170.12850.5797-0.1654-0.00170.3796-0.7319-1.21170.16070.94460.3423-0.23050.7520.05810.7197-24.918227.3852-9.598
20.8761-0.13310.06260.79250.67453.9294-0.0015-0.01720.0763-0.0623-0.17310.2827-0.309-0.61270.14490.65780.105-0.03140.4569-0.03060.4792-12.780517.1543-0.7402
32.36511.71962.22171.70651.87842.2388-2.6246-1.6241-1.462-4.20571.7636-2.1035-1.6251-1.72460.85030.5891-0.16440.09130.4506-0.05210.6651-10.449313.76740.3672
43.5390.0199-1.69012.47660.80273.64030.07760.16280.0767-0.4664-0.0386-0.1181-0.05310.1048-0.04420.7291-0.00590.04580.3305-0.01410.3912-9.1241-19.4072-87.4301
50.7299-0.6742-0.48042.2071.36891.3918-0.01320.13520.0506-0.2786-0.09770.1086-0.0737-0.10320.13140.4629-0.0204-0.0150.30150.03530.3039-21.8874-1.3271-70.4621
63.3472-1.4670.47272.50220.41142.92350.19930.4640.2121-0.5585-0.32680.3419-0.3269-0.78270.12660.55120.0635-0.12250.61480.07580.485-35.877425.774-72.3557
70.9413-0.6368-0.57462.16941.70464.74090.10.23250.1027-0.2033-0.24550.3043-0.1355-0.46730.15960.38870.0035-0.04220.3763-0.00810.4724-33.903820.5146-60.7665
85.62585.72483.89075.82543.95912.6908-1.77040.01980.6537-2.5590.980.1428-0.9698-0.38550.92810.3168-0.1225-0.08870.5613-0.11610.5003-31.064617.6383-59.7089
93.66242.19131.43913.10860.52441.5384-0.1274-0.1989-0.104-0.04740.0654-0.1145-0.22940.01760.07010.80740.08880.0810.4391-0.06120.44785.513129.954922.5982
100.87420.29530.29171.90330.84841.45550.1141-0.0741-0.1010.36120.0516-0.13010.16150.0325-0.17750.64720.0338-0.05860.3797-0.00320.40852.683-6.18116.5269
110.66750.16180.14210.89410.1370.89630.0637-0.1221-0.25770.57080.0305-0.11740.46410.0023-0.09190.91380.0728-0.12380.4071-0.01770.53192.0575-26.45826.3175
125.7022-2.6922-4.25678.33997.59857.59620.6553-1.72730.4851-0.44660.1013-0.18120.00991.736-0.71110.79810.0197-0.33470.4628-0.02440.72630.9227-18.14191.104
132.87350.9098-0.00514.5490.33182.02950.0289-0.22390.22360.18150.1362-0.19380.13670.1424-0.16110.38860.0088-0.0060.3429-0.08840.338-15.489431.8805-39.2143
141.1333-0.67010.03041.72610.08940.7879-0.089-0.0256-0.14490.0920.0511-0.07340.06380.03950.0410.5128-0.00810.01130.30930.00370.3374-14.2387-13.1504-54.2805
151.15040.07410.16632.50070.27370.96110.0038-0.0557-0.09570.2002-0.13460.17050.0457-0.25110.10160.5602-0.0370.02480.36820.01520.3665-19.0282-14.5402-57.5404
161.99411.99931.99182.01021.98782.00450.8394-0.93980.2135-1.8566-0.2615-0.1739-1.00151.5888-0.61420.5437-0.00730.03720.442-0.04040.2735-17.6163-13.2108-58.9509
173.29681.0223-1.21532.95170.21971.5998-0.1320.5793-0.3352-0.04320.2709-0.4511-0.00980.0101-0.13310.516-0.0032-0.02160.5991-0.22480.57210.8623-23.0895-26.0547
182.33411.0398-0.80882.6451.32971.8934-0.21810.81-0.4305-0.13490.2955-0.6217-0.1701-0.0617-0.07310.5345-0.0333-0.01780.6739-0.2170.4987.0965-22.0516-28.1172
191.3518-0.03680.1212.07820.82292.0667-0.00270.0830.0866-0.0376-0.04440.0272-0.20520.00250.03890.52830.0455-0.03120.33870.02360.3769-4.17748.2024-3.6051
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 321 through 376 )C321 - 376
2X-RAY DIFFRACTION2chain 'C' and (resid 377 through 497 )C377 - 497
3X-RAY DIFFRACTION3chain 'C' and (resid 601 through 601 )C601
4X-RAY DIFFRACTION4chain 'D' and (resid 10 through 100 )D10 - 100
5X-RAY DIFFRACTION5chain 'D' and (resid 101 through 281 )D101 - 281
6X-RAY DIFFRACTION6chain 'D' and (resid 282 through 376 )D282 - 376
7X-RAY DIFFRACTION7chain 'D' and (resid 377 through 498 )D377 - 498
8X-RAY DIFFRACTION8chain 'D' and (resid 601 through 601 )D601
9X-RAY DIFFRACTION9chain 'A' and (resid 11 through 143 )A11 - 143
10X-RAY DIFFRACTION10chain 'A' and (resid 144 through 320 )A144 - 320
11X-RAY DIFFRACTION11chain 'A' and (resid 321 through 497 )A321 - 497
12X-RAY DIFFRACTION12chain 'A' and (resid 601 through 601 )A601
13X-RAY DIFFRACTION13chain 'B' and (resid 9 through 172 )B9 - 172
14X-RAY DIFFRACTION14chain 'B' and (resid 173 through 409 )B173 - 409
15X-RAY DIFFRACTION15chain 'B' and (resid 410 through 498 )B410 - 498
16X-RAY DIFFRACTION16chain 'B' and (resid 601 through 601 )B601
17X-RAY DIFFRACTION17chain 'C' and (resid 11 through 89 )C11 - 89
18X-RAY DIFFRACTION18chain 'C' and (resid 90 through 172 )C90 - 172
19X-RAY DIFFRACTION19chain 'C' and (resid 173 through 320 )C173 - 320

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