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- PDB-6ns0: Crystal Structure of Lysyl-tRNA Synthetase from Chlamydia trachom... -

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Basic information

Entry
Database: PDB / ID: 6ns0
TitleCrystal Structure of Lysyl-tRNA Synthetase from Chlamydia trachomatis complexed with L-lysine and Cladosporin
ComponentsLysine--tRNA ligase
KeywordsLIGASE / SSGCID / KRS / nucleotide binding / Aminoacyl TRNA Ligase Activity / Lysine TRNA Ligase Activity / ATP Binding / Lysyl TRNA Aminoacylation / cladosporin / strain UCH-1/proctitis / strain D/UW-3/Cx) / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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, N-terminal / Lysine-tRNA ligase, class II / 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, N-terminal / Lysine-tRNA ligase, class II / 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 / DI(HYDROXYETHYL)ETHER / Lysine--tRNA ligase
Similarity search - Component
Biological speciesChlamydia trachomatis serovar L2b
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Lysyl-tRNA Synthetase from Chlamydia trachomatis with complexed with L-lysine and Cladosporin
Authors: Dranow, D.M. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJan 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,93246
Polymers122,3662
Non-polymers3,56544
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17770 Å2
ΔGint37 kcal/mol
Surface area39970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.580, 57.510, 139.550
Angle α, β, γ (deg.)90.000, 97.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 61183.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis serovar L2b (strain UCH-1/proctitis) (bacteria)
Strain: UCH-1/proctitis / Gene: lysS, CTLon_0150 / Plasmid: ChtrA.00612.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B0BAN6, lysine-tRNA ligase

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Non-polymers , 8 types, 507 molecules

#2: Chemical ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C16H20O5
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 3.14 Å3/Da / Density % sol: 60.87 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: ChtrA.00612.a.B1.PW38393 at 25.76 mg/ml was incubated with 3 mM l-lysine, 3 mM cladosporin, then was mixed 1:1 MorpheusB6opt1(e11): 10.96% (w/v) PEG 8000, 21.92% (v/v) ethylene glycol, 0.03 ...Details: ChtrA.00612.a.B1.PW38393 at 25.76 mg/ml was incubated with 3 mM l-lysine, 3 mM cladosporin, then was mixed 1:1 MorpheusB6opt1(e11): 10.96% (w/v) PEG 8000, 21.92% (v/v) ethylene glycol, 0.03 M each sodium fluoride, sodium bromide, sodium iodide, 0.1 M MOPE/HEPES-Na, pH=7.5. Tray: 300519e11, puck: ytb8-10. Crystallization of protein from strain UCH-1/proctitis and strain D/UW-3/Cx gave the same data.

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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: May 31, 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: 2.2→49.316 Å / Num. obs: 77679 / % possible obs: 99.8 % / Redundancy: 3.79 % / Biso Wilson estimate: 46.243 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.074 / Χ2: 1.009 / Net I/σ(I): 13.15 / Num. measured all: 294420 / Scaling rejects: 16
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
2.2-2.263.810.5772.3521603568056700.7970.67299.8
2.26-2.323.8180.4552.9621350559255920.8640.53100
2.32-2.393.8120.3773.5920735543854390.8980.439100
2.39-2.463.8220.3134.2819992523352310.930.365100
2.46-2.543.8190.2475.319494510951050.9520.28899.9
2.54-2.633.8190.2046.4218798493149220.9660.23899.8
2.63-2.733.8170.177.5718277479047880.9730.199100
2.73-2.843.8090.1359.2517500460445940.9830.15899.8
2.84-2.973.810.10411.7916740440043940.990.12299.9
2.97-3.113.8020.08513.9415954420141960.9930.09999.9
3.11-3.283.7990.06617.2215258402340160.9950.07799.8
3.28-3.483.7880.05520.2714343379737860.9960.06599.7
3.48-3.723.7830.04623.6813544358435800.9970.05499.9
3.72-4.023.7840.04226.0112698336633560.9970.04999.7
4.02-4.43.7630.03928.7511551308230700.9970.04599.6
4.4-4.923.7530.03729.8710433278827800.9970.04399.7
4.92-5.683.7250.03828.949265249624870.9970.04499.6
5.68-6.963.7080.03828.257783210720990.9970.04499.6
6.96-9.843.640.03431.395992165416460.9980.0499.5
9.84-49.3163.3510.03331.9331109529280.9970.0497.5

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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: 3A74

3a74


Resolution: 2.2→49.316 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.62
RfactorNum. reflection% reflectionSelection details
Rfree0.2073 1999 2.57 %RANDOM
Rwork0.1641 ---
obs0.1652 77666 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 155.54 Å2 / Biso mean: 53.1738 Å2 / Biso min: 21.27 Å2
Refinement stepCycle: final / Resolution: 2.2→49.316 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8027 0 234 466 8727
Biso mean--59.91 50.55 -
Num. residues----1034
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 (%)
2.2-2.25510.28251470.226353285475100
2.2551-2.3160.26971530.209553935546100
2.316-2.38420.25211330.19553805513100
2.3842-2.46110.28441250.192153675492100
2.4611-2.54910.22211450.184853765521100
2.5491-2.65120.25451490.183953525501100
2.6512-2.77180.25341250.184954125537100
2.7718-2.91790.26341500.177653825532100
2.9179-3.10070.2231350.174653855520100
3.1007-3.34010.20151720.17354075579100
3.3401-3.67610.20691300.159954195549100
3.6761-4.20780.16981410.141854395580100
4.2078-5.30040.15611500.131554375587100
5.3004-49.32820.21051440.16445590573499
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)
10.47050.16270.37470.67540.38113.2745-0.05070.1991-0.0466-0.5999-0.07010.00310.2479-0.12640.12310.8750.0633-0.01390.46260.01380.36089.8576-3.03728.0055
21.0722-0.2003-0.32190.7917-0.06051.17970.04240.06950.014-0.1561-0.05540.10480.0539-0.19840.01170.2325-0.0011-0.04920.2530.00180.25970.61474.874251.9746
34.05873.70321.8015.79730.60241.2468-0.3001-1.98161.9417-2.1869-1.83663.4319-0.5374-1.37332.15090.2440.0068-0.07540.2711-0.02350.32965.39463.619152.81
43.40641.23690.42853.7128-0.04231.59650.0279-0.05260.11130.1429-0.0873-0.3242-0.04770.16010.05320.1789-0.0132-0.05020.3541-0.00350.33327.407517.637669.2459
50.82160.2102-0.01481.0145-0.11372.08960.03160.147-0.1774-0.4348-0.068-0.28130.69260.3604-0.04960.60930.17830.09020.34160.02170.404425.8999-14.283233.2269
62.28872.44593.51833.95871.88578.01951.1047-0.3913-0.8287-2.1748-0.76221.24176.7033.271-0.32760.86860.1204-0.07120.4176-0.03030.468521.5467-14.903629.3915
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 208 )A4 - 208
2X-RAY DIFFRACTION2chain 'A' and (resid 209 through 520 )A209 - 520
3X-RAY DIFFRACTION3chain 'A' and (resid 601 through 601 )A601
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 167 )B4 - 167
5X-RAY DIFFRACTION5chain 'B' and (resid 168 through 520 )B168 - 520
6X-RAY DIFFRACTION6chain 'B' and (resid 601 through 601 )B601

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