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- PDB-6ncr: Crystal Structure of Tryptophan-tRNA ligase from Chlamydia tracho... -

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Basic information

Entry
Database: PDB / ID: 6ncr
TitleCrystal Structure of Tryptophan-tRNA ligase from Chlamydia trachomatis with bound L-tryptophan
ComponentsTryptophan--tRNA ligase
KeywordsLIGASE / SSGCID / Tryptophan--tRNA ligase / L-tryptophan / ATP binding / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / ATP binding / cytoplasm
Similarity search - Function
Tryptophan-tRNA ligase, bacterial-type / Tryptophan-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / Orthogonal Bundle ...Tryptophan-tRNA ligase, bacterial-type / Tryptophan-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / TRYPTOPHAN / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Tryptophan-tRNA ligase from Chlamydia trachomatis with bound L-tryptophan
Authors: Dranow, D.M. / Mayclin, S.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionDec 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2018Provider: 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)82,64822
Polymers81,1632
Non-polymers1,48620
Water7,152397
1
A: Tryptophan--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,50514
Polymers40,5811
Non-polymers92413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tryptophan--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1438
Polymers40,5811
Non-polymers5627
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8320 Å2
ΔGint-23 kcal/mol
Surface area29810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.890, 61.050, 246.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 40581.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (strain D/UW-3/Cx) (bacteria)
Strain: D/UW-3/Cx / Gene: trpS, CT_585 / Plasmid: ChtrB.00743.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O84589, tryptophan-tRNA ligase

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Non-polymers , 5 types, 417 molecules

#2: Chemical ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: ChtrB.00743.a.B1.PW38496 at 17.16 mg/ml was incubated with 3 mM L-Trp, magnesium chloride, and AMPPNP, then was mixed 1:1 with MCSG1(c11): 20.0% (w/v) PEG 3000, 0.2 M calcium acetate, 0.1 M ...Details: ChtrB.00743.a.B1.PW38496 at 17.16 mg/ml was incubated with 3 mM L-Trp, magnesium chloride, and AMPPNP, then was mixed 1:1 with MCSG1(c11): 20.0% (w/v) PEG 3000, 0.2 M calcium acetate, 0.1 M Tris base/ HCl, pH=7.0 and cryoprotected with 20% ethylene glycol. Tray: 302466c11, puck: xcr5-13

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.75→47.029 Å / Num. obs: 78460 / % possible obs: 99.8 % / Redundancy: 6.322 % / Biso Wilson estimate: 38.366 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.04 / Χ2: 1.094 / Net I/σ(I): 23.41 / Num. measured all: 496022 / Scaling rejects: 281
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
1.75-1.86.3610.6092.4736571575157490.8410.664100
1.8-1.846.2490.4993.0734874558155810.8920.544100
1.84-1.96.4110.3963.9334684541554100.9280.43299.9
1.9-1.966.4720.3035.2934283529852970.9580.33100
1.96-2.026.5040.2267.1133228511851090.9780.24699.8
2.02-2.096.6790.16710.0733193497049700.9880.181100
2.09-2.176.5060.12713.2131127478647840.9930.139100
2.17-2.266.3170.09916.929255464246310.9950.10899.8
2.26-2.366.4880.07921.4228749443644310.9970.08699.9
2.36-2.476.3370.06725.1826953426042530.9970.07399.8
2.47-2.616.5750.05729.6726504403240310.9980.062100
2.61-2.776.2480.04734.2724200387638730.9990.05199.9
2.77-2.966.0540.03940.4121934362836230.9990.04399.9
2.96-3.25.910.03445.3419936339733730.9990.03799.3
3.2-3.56.2330.0352.4219260310730900.9990.03299.5
3.5-3.915.9560.02556.8216968286528490.9990.02799.4
3.91-4.525.9550.02260.5814941252525090.9990.02499.4
4.52-5.536.1420.0261.5133402180217210.02299.6
5.53-7.835.990.01959.7810278172017160.9990.0299.8
7.83-47.0295.6930.01561.7757441019100910.01699

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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: 2G36

2g36


Resolution: 1.75→47.029 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.34
RfactorNum. reflection% reflection
Rfree0.1958 1971 2.51 %
Rwork0.171 --
obs0.1717 78451 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 116.04 Å2 / Biso mean: 41.9114 Å2 / Biso min: 17.47 Å2
Refinement stepCycle: final / Resolution: 1.75→47.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5340 0 99 399 5838
Biso mean--55.52 45.82 -
Num. residues----683
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 (%)
1.7499-1.79370.32151260.249653795505100
1.7937-1.84220.28221350.222653915526100
1.8422-1.89640.21851220.211754455567100
1.8964-1.95760.22121530.196253795532100
1.9576-2.02750.2341360.195154005536100
2.0275-2.10870.22461570.184754005557100
2.1087-2.20470.20971460.17654315577100
2.2047-2.32090.22811250.170554275552100
2.3209-2.46630.23631370.180254295566100
2.4663-2.65670.21231440.186554935637100
2.6567-2.92410.21281410.180754615602100
2.9241-3.34710.21391380.17545486562499
3.3471-4.21660.17171420.15195565570799
4.2166-47.04550.15931690.154257945963100
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)
11.28180.3556-0.96941.9435-0.72252.80990.03870.15150.0851-0.0731-0.0328-0.0425-0.14340.0661-0.00010.17230.0329-0.02190.2410.03140.20169.74121.861518.7838
21.65670.70750.2460.63890.32441.5737-0.07850.25280.3268-0.00780.07110.2409-0.4091-0.12430.03270.23630.0510.00450.21840.05330.2669-0.514524.420427.1367
33.3073-3.16411.75734.7472-2.64522.49220.09580.20660.0255-0.476-0.05250.2998-0.29060.036-0.04680.5650.0425-0.07020.40130.07030.30495.995738.6138-4.5278
40.80780.9477-1.16681.0898-1.26534.12210.07080.0032-0.08310.1458-0.2457-0.1857-0.05880.38520.22890.17420.0391-0.04310.28340.02710.279917.098213.546833.2937
52.63342.21232.84722.00012.38373.83220.10041.02660.3776-0.7414-0.0435-0.2561-0.30690.3004-0.06940.29350.07340.03460.3532-0.01380.26895.246223.39620.2038
62.2442-0.4134-1.90264.45122.2167.35850.19390.1538-0.128-0.3220.0473-0.2969-0.2027-0.1398-0.21770.3370.026-0.08750.23480.0150.2967-2.318-10.65141.3209
71.08690.0176-0.03192.3087-0.56411.79770.037-0.0554-0.16860.0888-0.0449-0.07770.34950.0570.02210.32090.0161-0.02420.20720.01310.20611.8996-4.824845.1483
83.6619-0.37140.59363.323-0.21053.31050.0726-0.17890.05120.21780.00050.70420.1188-0.65360.04560.2138-0.02060.07340.31190.02410.3484-8.38358.245831.1108
93.8686-0.54640.56535.8092-0.25923.02690.01370.0778-0.12460.3286-0.01380.19050.4311-0.341-0.03910.2634-0.04020.01220.21110.00610.1618-4.1937-1.723432.1695
100.38930.4225-0.95680.9653-2.74517.8407-0.13230.1253-0.0019-0.04330.25440.10770.2362-0.8504-0.07940.3163-0.0217-0.05580.29310.00890.3021-8.3599-5.007737.1389
114.28110.6839-1.44213.5378-0.29254.1814-0.06670.1379-0.46510.1969-0.09840.71220.4444-0.85650.11840.4037-0.1079-0.03040.3681-0.02540.3522-16.0414-15.638964.3178
120.44320.5889-1.97752.5248-3.20199.0763-0.0672-0.1245-0.1425-0.1848-0.256-0.32330.56690.60960.4240.22560.11510.00560.29770.0050.323313.5897-0.950427.7856
137.5527-7.8183-2.97098.68965.02077.80120.45650.22510.3668-0.2614-0.43660.0493-0.1526-0.7274-0.15810.48830.0986-0.05190.52040.01510.5969-4.7903-2.169338.8744
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 112 )A2 - 112
2X-RAY DIFFRACTION2chain 'A' and (resid 113 through 192 )A113 - 192
3X-RAY DIFFRACTION3chain 'A' and (resid 193 through 302 )A193 - 302
4X-RAY DIFFRACTION4chain 'A' and (resid 303 through 343 )A303 - 343
5X-RAY DIFFRACTION5chain 'A' and (resid 401 through 401 )A401
6X-RAY DIFFRACTION6chain 'B' and (resid -1 through 24 )B-1 - 24
7X-RAY DIFFRACTION7chain 'B' and (resid 25 through 90 )B25 - 90
8X-RAY DIFFRACTION8chain 'B' and (resid 91 through 130 )B91 - 130
9X-RAY DIFFRACTION9chain 'B' and (resid 131 through 159 )B131 - 159
10X-RAY DIFFRACTION10chain 'B' and (resid 160 through 215 )B160 - 215
11X-RAY DIFFRACTION11chain 'B' and (resid 216 through 303 )B216 - 303
12X-RAY DIFFRACTION12chain 'B' and (resid 304 through 345 )B304 - 345
13X-RAY DIFFRACTION13chain 'B' and (resid 401 through 401 )B401

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