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- PDB-6vu9: Crystal structure of threonyl-tRNA synthetase (ThrRS) from Stenot... -

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Basic information

Entry
Database: PDB / ID: 6vu9
TitleCrystal structure of threonyl-tRNA synthetase (ThrRS) from Stenotrophomonas maltophilia K279a
ComponentsThreonine--tRNA ligase
KeywordsLIGASE / AARS / aminoacyl tRNA synthetase / NIAID / National Institute of Allergy and Infectious Diseases / thrS / antibiotic resistance / borrelidin / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl and Alanyl tRNA synthetase second additional domain / TGS domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS domain profile. / TGS / TGS-like ...Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl and Alanyl tRNA synthetase second additional domain / TGS domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS domain profile. / TGS / TGS-like / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Beta-grasp domain superfamily
Similarity search - Domain/homology
Threonine--tRNA ligase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of threonyl-tRNA synthetase (ThrRS) from Stenotrophomonas maltophilia K279a
Authors: Edwards, T.E. / Dranow, D.M. / Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionFeb 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

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Assembly

Deposited unit
A: Threonine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2974
Polymers73,0401
Non-polymers2583
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.070, 163.930, 76.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-701-

SO4

21A-920-

HOH

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Components

#1: Protein Threonine--tRNA ligase / Threonyl-tRNA synthetase / ThrRS


Mass: 73039.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria)
Strain: K279a / Gene: thrS, Smlt3378 / Production host: Escherichia coli (E. coli) / References: UniProt: B2FN79, threonine-tRNA ligase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.65 Å3/Da / Density % sol: 53.63 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: StmaA.00156.a.B1.PW38695 at mg/mL against MCSG1 screen condition C8: 0.2 sodium sulfate, 0.1 M sodium citrate pH 5.6, 20% PEG 4000 supplemented with 15% ethylene glycol as cryoprotectant, ...Details: StmaA.00156.a.B1.PW38695 at mg/mL against MCSG1 screen condition C8: 0.2 sodium sulfate, 0.1 M sodium citrate pH 5.6, 20% PEG 4000 supplemented with 15% ethylene glycol as cryoprotectant, unique puck ID ygn6-7, crystal ID 312751c8

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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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.2→39.8 Å / Num. obs: 39658 / % possible obs: 99.6 % / Redundancy: 8.26 % / Biso Wilson estimate: 56.017 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.042 / Χ2: 1.026 / Net I/σ(I): 28.45 / Num. measured all: 327591 / Scaling rejects: 4
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
2.2-2.268.4270.5992.9524236289728760.9520.63899.3
2.26-2.328.4190.4743.7923768283828230.9610.50499.5
2.32-2.398.420.3535.0123138276327480.980.37699.5
2.39-2.468.4250.2826.1422597270126820.9870.30199.3
2.46-2.548.4490.2237.821503255925450.9920.23799.5
2.54-2.638.3930.1741021242254425310.9950.18699.5
2.63-2.738.4010.1412.520532245324440.9960.14999.6
2.73-2.848.3880.10316.519585234723350.9980.1199.5
2.84-2.978.3650.08720.2518655223922300.9980.09299.6
2.97-3.118.3460.06227.1717943215321500.9990.06699.9
3.11-3.288.3230.04636.5617079205720520.9990.04999.8
3.28-3.488.2680.03644.1416147195519530.9990.03999.9
3.48-3.728.2040.0354.46149481824182210.03299.9
3.72-4.028.1060.02761.59139431724172010.02999.8
4.02-4.48.0330.02469.7126521578157510.02699.8
4.4-4.927.9280.02173.25114321442144210.022100
4.92-5.687.8550.02273.33100391278127810.024100
5.68-6.967.6870.02273.2884021093109310.023100
6.96-9.847.5750.01978.93657586986810.02199.9
9.84-39.86.4660.02175.6131755124910.9990.02395.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MR-Rosettaphasing
PHENIX1.17.1-3660refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4htA

4hta


Resolution: 2.2→39.8 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.03
RfactorNum. reflection% reflection
Rfree0.2291 2033 5.14 %
Rwork0.19 --
obs0.192 39585 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 156.4 Å2 / Biso mean: 73.2172 Å2 / Biso min: 23.65 Å2
Refinement stepCycle: final / Resolution: 2.2→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4839 0 11 121 4971
Biso mean--62.36 59.14 -
Num. residues----631
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 (%)
2.2-2.250.36411220.2722476259899
2.25-2.310.35161470.25442430257799
2.31-2.370.32421350.24332476261199
2.37-2.440.30651350.23932448258399
2.44-2.520.23221230.22322475259899
2.52-2.610.26491280.21852484261299
2.61-2.710.26831280.21812486261499
2.71-2.840.26411360.21992505264199
2.84-2.990.24671370.223824802617100
2.99-3.170.24651310.216725092640100
3.17-3.420.22021280.209125322660100
3.42-3.760.21661450.189824992644100
3.76-4.30.21681340.166425522686100
4.31-5.420.16891550.154125402695100
5.42-39.80.24221490.17126602809100
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)
14.42070.28060.88171.1688-0.39162.5009-0.4044-0.3312-0.69040.0393-0.0049-0.1113-0.152-0.22260.3710.5640.06480.02720.47030.04290.89544.8017-47.3342-4.8203
20.60060.3916-1.44762.5933-2.75170.4196-0.0726-0.007-0.59650.1024-0.2658-0.27050.01480.19040.31290.8384-0.0692-0.24260.50510.07040.72613.8262-28.1871-15.1624
32.3811-0.15070.00332.26810.56542.18370.1760.3487-0.4914-0.17550.0099-0.32320.3443-0.0552-0.16640.39740.0028-0.03420.3171-0.04960.385818.9801-13.2616-49.048
43.82980.22620.33183.17420.13883.35460.5375-0.96090.28230.5520.0519-0.94810.06810.7067-0.55450.7831-0.0467-0.28931.023-0.07631.172843.7392-5.5853-17.946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 181 )A3 - 181
2X-RAY DIFFRACTION2chain 'A' and (resid 182 through 267 )A182 - 267
3X-RAY DIFFRACTION3chain 'A' and (resid 268 through 541 )A268 - 541
4X-RAY DIFFRACTION4chain 'A' and (resid 542 through 633 )A542 - 633

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