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- PDB-6aqg: Crystal Structure of Lysyl-tRNA Synthetase from Mycobacterium ulc... -

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Basic information

Entry
Database: PDB / ID: 6aqg
TitleCrystal Structure of Lysyl-tRNA Synthetase from Mycobacterium ulcerans 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 / tRNA binding / magnesium ion binding / ATP binding / cytosol
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 ulcerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Lysyl-tRNA Synthetase from Mycobacterium ulcerans 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)229,14821
Polymers226,3264
Non-polymers2,82217
Water17,691982
1
A: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3766
Polymers56,5821
Non-polymers7945
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4947
Polymers56,5821
Non-polymers9126
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1394
Polymers56,5821
Non-polymers5583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1394
Polymers56,5821
Non-polymers5583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Lysine--tRNA ligase
D: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,51510
Polymers113,1632
Non-polymers1,3528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10140 Å2
ΔGint-87 kcal/mol
Surface area38040 Å2
MethodPISA
6
B: Lysine--tRNA ligase
C: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,63311
Polymers113,1632
Non-polymers1,4709
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10300 Å2
ΔGint-93 kcal/mol
Surface area38180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.120, 97.200, 105.830
Angle α, β, γ (deg.)90.050, 104.280, 117.860
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 56581.621 Da / Num. of mol.: 4 / Fragment: MyulA.00612.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium ulcerans (strain Agy99) (bacteria)
Strain: Agy99 / Gene: lysS, MUL_4181 / Plasmid: MyulA.00612.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0PV47, 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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 982 / 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: 3.63 Å3/Da / Density % sol: 66.13 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9.1
Details: MyulA.00612.a.B1.PW37993 at 28 mg/ml was incubated with 3 mM L-Lysine and cladosporin, then mixed 1:1 with MorpheusCol12opt1 (h7): 0.1 M Tris base/ HCl, pH=9.1, 12.5% (w/v) PEG-1000, 16% ...Details: MyulA.00612.a.B1.PW37993 at 28 mg/ml was incubated with 3 mM L-Lysine and cladosporin, then mixed 1:1 with MorpheusCol12opt1 (h7): 0.1 M Tris base/ HCl, pH=9.1, 12.5% (w/v) PEG-1000, 16% (w/v) PEG-3350, 12.5% (v/v) MPD. Tray: 291151h7, puck: wer4-8

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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: Aug 7, 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: 2.25→41.316 Å / Num. obs: 148550 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 3.885 % / Biso Wilson estimate: 45.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.069 / Χ2: 1.043 / Net I/σ(I): 12.66
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.25-2.313.9470.5632.23108920.8040.65297.5
2.31-2.373.9470.4522.78106400.8670.52397.6
2.37-2.443.9510.3633.43103440.9040.4297.8
2.44-2.523.9440.2834.24100850.9460.32897.9
2.52-2.63.9380.2245.3497850.9620.2698
2.6-2.693.9350.1886.3794790.9730.21898.1
2.69-2.793.9180.1478.0291240.9810.1798.3
2.79-2.93.9140.11510.0187990.9880.13398.3
2.9-3.033.8960.09312.385380.9910.10898.4
3.03-3.183.8860.07515.0980180.9940.08798.6
3.18-3.353.8560.06417.5877650.9950.07498.7
3.35-3.563.8370.05420.3272400.9960.06398.7
3.56-3.83.8310.04822.7268790.9960.05698.7
3.8-4.113.8160.04524.3764250.9970.05298.8
4.11-4.53.8080.04126.0758750.9970.04899
4.5-5.033.7860.0426.5553250.9970.04699.2
5.03-5.813.780.04226.2946940.9970.04999.1
5.81-7.123.7660.04226.3339750.9970.04899.3
7.12-10.063.7520.03527.8930690.9980.04199.2
10.06-41.3163.5370.03527.4915990.9970.04194.4

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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: 2.25→41.316 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 19.95
RfactorNum. reflection% reflection
Rfree0.1949 1954 1.32 %
Rwork0.1531 --
obs0.1536 148513 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 141.1 Å2 / Biso mean: 54.3156 Å2 / Biso min: 16.87 Å2
Refinement stepCycle: final / Resolution: 2.25→41.316 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15058 0 196 986 16240
Biso mean--60.77 51.68 -
Num. residues----1951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715567
X-RAY DIFFRACTIONf_angle_d0.84521162
X-RAY DIFFRACTIONf_chiral_restr0.0512412
X-RAY DIFFRACTIONf_plane_restr0.0062772
X-RAY DIFFRACTIONf_dihedral_angle_d16.7159353
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 (%)
2.25-2.30630.26791220.2213103821050497
2.3063-2.36860.23921330.202103921052598
2.3686-2.43830.23621430.1889104071055098
2.4383-2.5170.21861510.1806104081055998
2.517-2.6070.23071350.173104351057098
2.607-2.71130.24661520.1731104751062798
2.7113-2.83470.23411510.1735104231057498
2.8347-2.98410.18351260.1703105011062798
2.9841-3.1710.2271470.1712104881063599
3.171-3.41570.20921470.1681105521069999
3.4157-3.75930.20521500.1548104811063199
3.7593-4.30270.17461410.1336105201066199
4.3027-5.41910.15341400.1208105661070699
5.4191-41.3230.17111160.1421105291064599
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)
12.35870.15-0.23825.090.0581.9845-0.16730.4703-0.609-0.4848-0.20720.02060.4069-0.57740.32690.5536-0.10340.06410.4848-0.17750.49291.7833-24.3323-28.146
20.7184-0.0501-0.25830.95370.95822.78450.07250.064-0.054-0.1601-0.0482-0.0422-0.019-0.1323-0.01940.2468-0.00260.01160.22840.04930.28018.5034-3.44990.0303
30.47610.26060.46780.97380.35741.20840.09680.00610.1189-0.13040.0784-0.2095-0.26850.2293-0.180.2819-0.04740.0610.2811-0.00810.338119.87898.747515.2735
41.94431.1614-1.31015.0428-4.85284.71980.0256-1.24840.9732-1.30260.0889-0.23550.55112.0611-0.06550.2982-0.0529-0.00380.43450.03630.37611.01247.831411.9757
54.32360.1905-1.08743.9697-1.42634.2363-0.0215-0.882-0.10931.0516-0.186-0.0926-0.39320.24240.18330.71030.0624-0.17880.620.02010.40334.609943.2064-7.5105
63.8786-0.9930.54081.8694-0.7911.178-0.1895-0.3972-0.37820.2683-0.2813-0.8288-0.07120.83530.37160.38860.0132-0.07570.75810.20980.690815.755634.126-14.9931
71.64790.9024-0.8955.7343-4.98224.6078-0.1381-0.1798-0.32060.1029-0.1477-0.30560.20460.56930.23930.24710.0262-0.04030.3460.00250.3134-3.302836.8279-33.9317
81.7811-0.6841-0.09672.3034-0.31423.3739-0.098-0.0919-0.08170.15920.08680.08-0.151-0.0849-0.00270.1588-0.0189-0.00350.2409-0.00440.2254-12.301947.188-49.4153
91.60330.50560.23652.79660.44741.14050.04790.0119-0.07560.0988-0.06210.37010.0591-0.3835-0.00150.2298-0.03340.01440.34660.02160.2865-25.865241.0121-60.6042
100.8322-0.83261.11112.2808-1.47032.5089-0.0658-0.2441-0.12180.10810.19090.20620.33-0.2317-0.18840.28010.01940.03730.3482-0.00320.3556-11.273938.8705-41.3441
113.23731.89962.88511.66131.69612.5736-1.21880.17880.7157-0.68581.94681.19462.8179-2.3916-0.62980.3704-0.01790.0070.4623-0.01990.3274-17.787447.4901-53.5623
123.73060.6348-1.03452.9146-1.39163.85360.09150.15280.1176-0.2925-0.1016-0.1331-0.157-0.0216-0.00430.4118-0.0019-0.00250.24730.0580.2935-8.690467.0646-76.9586
134.2361-1.15653.25941.2378-1.814.5576-0.2618-0.16810.41960.21810.0409-0.072-0.94580.06560.20720.5982-0.0498-0.00240.2646-0.00590.4282-7.446368.482-51.6229
144.8829-0.50690.80351.7238-0.97612.8288-0.0737-0.15360.26640.35220.0956-0.0501-0.4232-0.0979-0.03760.42020.01030.01780.2323-0.03380.2171-9.733653.8729-29.6441
151.53590.54880.12342.87620.50382.20570.0606-0.46040.6750.6803-0.116-0.0066-0.77470.3157-0.00880.8411-0.1532-0.11440.4998-0.1560.67521.472771.8145-19.8897
160.9974-0.26830.09631.4891-1.0373.5325-0.1231-0.27150.26790.39180.0783-0.0356-0.746-0.05960.03740.5802-0.0006-0.03860.3668-0.07980.363-7.413760.5051-24.736
176.81771.07577.31472.33161.38017.8719-0.41020.42391.52070.53140.5145-0.41360.5348-0.7419-0.07020.6423-0.0359-0.02920.54890.0270.5106-4.622159.2799-24.6411
183.33480.2767-1.51192.79520.1613.7808-0.105-0.1583-0.06250.30820.12360.173-0.1823-0.2095-0.03550.28620.0860.05760.3732-0.00990.287-10.126811.404935.7396
190.29240.0554-0.250.86631.87364.24690.03330.05450.1238-0.0471-0.19860.2953-0.2956-0.71530.13660.32270.12220.00710.530.02680.4578-10.930410.676612.9239
201.44820.4392-0.51452.20980.91763.32170.12030.22880.2017-0.4078-0.12570.2223-0.4846-0.386-0.02330.35330.1094-0.02390.39590.05570.28340.8454.5071-11.7166
212.6896-0.17750.56751.684-0.13881.86070.06680.59820.3633-0.4713-0.09870.6214-0.2637-0.8756-0.03430.49860.1698-0.18480.93820.00590.675-20.33115.3036-21.2368
220.9771-0.3448-0.47571.24340.40323.06190.09480.30150.1355-0.392-0.07420.2513-0.4133-0.5467-0.02450.49030.1051-0.06810.57490.02480.4069-6.00065.8655-16.8382
236.1119-6.6016-2.1697.26422.72071.89691.19320.35540.5722-0.993-1.75961.9433-0.5929-1.32570.62460.51070.08640.01140.77290.07970.5638-6.52163.2917-16.5813
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 123 )A9 - 123
2X-RAY DIFFRACTION2chain 'A' and (resid 124 through 317 )A124 - 317
3X-RAY DIFFRACTION3chain 'A' and (resid 318 through 495 )A318 - 495
4X-RAY DIFFRACTION4chain 'A' and (resid 601 through 601 )A601
5X-RAY DIFFRACTION5chain 'B' and (resid 9 through 39 )B9 - 39
6X-RAY DIFFRACTION6chain 'B' and (resid 40 through 149 )B40 - 149
7X-RAY DIFFRACTION7chain 'B' and (resid 150 through 192 )B150 - 192
8X-RAY DIFFRACTION8chain 'B' and (resid 193 through 317 )B193 - 317
9X-RAY DIFFRACTION9chain 'B' and (resid 318 through 464 )B318 - 464
10X-RAY DIFFRACTION10chain 'B' and (resid 465 through 495 )B465 - 495
11X-RAY DIFFRACTION11chain 'B' and (resid 601 through 601 )B601
12X-RAY DIFFRACTION12chain 'C' and (resid 7 through 140 )C7 - 140
13X-RAY DIFFRACTION13chain 'C' and (resid 141 through 193 )C141 - 193
14X-RAY DIFFRACTION14chain 'C' and (resid 194 through 278 )C194 - 278
15X-RAY DIFFRACTION15chain 'C' and (resid 279 through 405 )C279 - 405
16X-RAY DIFFRACTION16chain 'C' and (resid 406 through 496 )C406 - 496
17X-RAY DIFFRACTION17chain 'C' and (resid 601 through 601 )C601
18X-RAY DIFFRACTION18chain 'D' and (resid 7 through 134 )D7 - 134
19X-RAY DIFFRACTION19chain 'D' and (resid 135 through 193 )D135 - 193
20X-RAY DIFFRACTION20chain 'D' and (resid 194 through 278 )D194 - 278
21X-RAY DIFFRACTION21chain 'D' and (resid 279 through 405 )D279 - 405
22X-RAY DIFFRACTION22chain 'D' and (resid 406 through 496 )D406 - 496
23X-RAY DIFFRACTION23chain 'D' and (resid 601 through 601 )D601

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