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

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Basic information

Entry
Database: PDB / ID: 6nrz
TitleCrystal Structure of Lysyl-tRNA Synthetase from Chlamydia trachomatis complexed with L-lysine and Adenosine
ComponentsLysine--tRNA ligase
KeywordsLIGASE / SSGCID / KRS / nucleotide binding / Aminoacyl TRNA Ligase Activity / Lysine TRNA Ligase Activity / ATP Binding / Lysyl TRNA Aminoacylation / 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
ADENOSINE / LYSINE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesChlamydia trachomatis serovar L2b
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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 Adenosine
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 20, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 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)125,40339
Polymers122,3662
Non-polymers3,03737
Water10,178565
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17180 Å2
ΔGint23 kcal/mol
Surface area39740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.170, 57.520, 139.090
Angle α, β, γ (deg.)90.000, 96.680, 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 , 7 types, 602 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-ADN / ADENOSINE / Adenosine


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-NA / SODIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 565 / 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: 3.12 Å3/Da / Density % sol: 60.61 %
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 adenosine, then was mixed 1:1 with MorpheusB6opt1(e12): 11.1% (w/v) PEG 8000, 22.2% (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 adenosine, then was mixed 1:1 with MorpheusB6opt1(e12): 11.1% (w/v) PEG 8000, 22.2% (v/v) ethylene glycol, 0.03 M each sodium fluoride, sodium bromide, sodium iodide, 0.1 M MOPE/HEPES-Na, pH=7.5. Tray: 300518e12, puck: ytb8-4. 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: 2.1→49.275 Å / Num. obs: 88632 / % possible obs: 99.8 % / Redundancy: 4.214 % / Biso Wilson estimate: 44.54 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.082 / Χ2: 0.989 / Net I/σ(I): 11.76 / Num. measured all: 373489 / Scaling rejects: 5
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
2.1-2.154.2360.5972.3527567652965080.7430.68399.7
2.15-2.214.2340.4593.0426901636863540.8440.52699.8
2.21-2.284.2460.3763.6726166616161630.8870.43100
2.28-2.354.2470.3084.5225387599259770.9210.35299.7
2.35-2.424.2310.2625.2824689584058350.940.29999.9
2.42-2.514.2380.2156.3623871564056330.9570.24699.9
2.51-2.64.2330.1717.7823065545654490.9740.19699.9
2.6-2.714.2460.146922028519251880.9790.16799.9
2.71-2.834.2380.11810.6821500508150730.9860.13599.8
2.83-2.974.2280.09513.0820193478147760.990.10999.9
2.97-3.134.2240.08115.1719403460045930.9920.09299.8
3.13-3.324.210.06717.9218205432943240.9930.07799.9
3.32-3.554.2060.05920.2917197409340890.9940.06799.9
3.55-3.834.2030.05222.4916017381438110.9950.0699.9
3.83-4.24.1920.04923.9214703351835070.9950.05699.7
4.2-4.74.180.04725.4713339319431910.9960.05499.9
4.7-5.424.160.04725.2211686281328090.9950.05599.9
5.42-6.644.1220.0524.189929241424090.9960.05799.8
6.64-9.394.0430.04625.647653190118930.9960.05399.6
9.39-49.2753.80.04725.863990107510500.9950.05597.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A74

3a74


Resolution: 2.1→49.275 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.56
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1995 2.25 %RANDOM
Rwork0.16 ---
obs0.1608 88605 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 128.91 Å2 / Biso mean: 51.3004 Å2 / Biso min: 19.58 Å2
Refinement stepCycle: final / Resolution: 2.1→49.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8063 0 199 569 8831
Biso mean--60.55 51.18 -
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 (%)
2.1001-2.15260.27391510.226561346285100
2.1526-2.21080.28731340.210861416275100
2.2108-2.27580.26991480.20161186266100
2.2758-2.34930.24941440.188561496293100
2.3493-2.43330.23331540.18361186272100
2.4333-2.53070.22341360.170561856321100
2.5307-2.64580.20241400.161161346274100
2.6458-2.78530.22331550.164261836338100
2.7853-2.95980.20171420.168361706312100
2.9598-3.18830.19691420.166461936335100
3.1883-3.50910.211290.165962026331100
3.5091-4.01670.18481480.147462206368100
4.0167-5.05980.14531410.12762636404100
5.0598-49.28880.1851310.15946400653199
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)
10.50980.03320.23720.85480.12962.9557-0.03890.2568-0.0432-0.5936-0.04930.0030.2787-0.11640.08730.65160.04520.03620.4453-0.01540.297810.1208-3.540412.6032
21.1911-0.1818-0.25250.7610.04961.13240.03950.14040.0257-0.1304-0.08210.09820.0456-0.22340.04210.2610.0051-0.0410.27710.00660.2877-0.03025.762851.9363
32.32912.18132.15433.41071.5012.1876-0.8991-1.85911.1407-3.3508-1.06922.6291-0.8404-0.88441.92390.34110.029-0.04080.2343-0.01260.36865.64873.540652.6579
43.1410.93990.24173.00030.08481.25250.0097-0.01890.13120.1726-0.0589-0.3478-0.04670.15330.03520.1841-0.0181-0.06370.278-0.00030.314727.592317.566269.0196
51.04840.08110.53041.24910.34863.24310.04640.1382-0.0659-0.2953-0.0738-0.25530.33930.09930.00950.32360.08240.07840.2348-0.00290.3121.4545-7.334737.7423
61.19380.28370.43750.71020.13151.54460.17790.2201-0.4823-0.29610.0054-0.47710.86160.3982-0.16060.75920.22380.09890.4286-0.02280.578230.1686-19.749629.7143
74.56561.25843.79242.30940.30414.24010.78810.0623-0.4064-1.0083-0.60930.41613.30781.8731-0.17050.70260.12450.01790.38-0.0110.453321.9749-14.906729.1587
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 235 )A4 - 235
2X-RAY DIFFRACTION2chain 'A' and (resid 236 through 520 )A236 - 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 313 )B168 - 313
6X-RAY DIFFRACTION6chain 'B' and (resid 314 through 520 )B314 - 520
7X-RAY DIFFRACTION7chain 'B' and (resid 601 through 601 )B601

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