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- PDB-6n0w: Crystal structure of a Tyrosine--tRNA ligase from Elizabethkingia... -

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Basic information

Entry
Database: PDB / ID: 6n0w
TitleCrystal structure of a Tyrosine--tRNA ligase from Elizabethkingia anophelis
ComponentsTyrosine--tRNA ligase
KeywordsLIGASE / NIAID / structural genomics / aminoacyl-tRNA ligase / large C-terminal disordered domain / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / RNA binding / ATP binding / cytoplasm
Similarity search - Function
Tyrosine-tRNA ligase, bacterial-type, type 1 / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Rossmann-like alpha/beta/alpha sandwich fold / RNA-binding S4 domain / RNA-binding S4 domain superfamily / S4 RNA-binding domain profile.
Similarity search - Domain/homology
Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesElizabethkingia anophelis NUHP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a Tyrosine--tRNA ligase from Elizabethkingia anophelis
Authors: Edwards, T.E. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionNov 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Oct 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: Tyrosine--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)53,5551
Polymers53,5551
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.290, 37.560, 81.760
Angle α, β, γ (deg.)90.000, 112.400, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Tyrosine--tRNA ligase / Tyrosyl-tRNA synthetase / TyrRS


Mass: 53555.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia anophelis NUHP1 (bacteria)
Gene: tyrS, BD94_1246, tyrS / Production host: Escherichia coli (E. coli) / References: UniProt: A0A077EBU6, tyrosine-tRNA ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS STATE THAT THE STRETCHES OF UNKNOWN RESIDUES (UNK) REPRESENT DIFFERENT UNASSIGNED ...THE AUTHORS STATE THAT THE STRETCHES OF UNKNOWN RESIDUES (UNK) REPRESENT DIFFERENT UNASSIGNED PORTIONS OF THE C-TERMINAL REGION OF THE TARGET PROTEIN IN CHAIN A.

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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: 2.61 Å3/Da / Density % sol: 52.91 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: ElanA.01032.a.B1.PW38270 at 26 mg/mL against the Morpheus screen condition D9: 10% PEG 20,000, 20% PEG 550 MME, 0.02 M each alcohol (1,6-hexanediol, 1-butanol, R,S-1,2-propanediol, 2- ...Details: ElanA.01032.a.B1.PW38270 at 26 mg/mL against the Morpheus screen condition D9: 10% PEG 20,000, 20% PEG 550 MME, 0.02 M each alcohol (1,6-hexanediol, 1-butanol, R,S-1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol), 0.1 M bicine/Trizma base pH 8.5, unique puck ID xyo1-1, crystal tracking ID 292624d9

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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: Aug 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.7→47.957 Å / Num. obs: 15648 / % possible obs: 99.6 % / Redundancy: 4.926 % / Biso Wilson estimate: 66.778 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.06 / Χ2: 1.022 / Net I/σ(I): 20.16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.7-2.775.080.6692.6311200.9050.746100
2.77-2.855.0040.553.1711340.9120.61599.7
2.85-2.935.0090.4493.9510690.9280.50199.6
2.93-3.025.0650.3125.610410.9660.34999.8
3.02-3.124.9680.2287.5710420.9850.25599.8
3.12-3.235.0640.1739.419860.990.19399.5
3.23-3.354.940.12512.889490.9940.14199.6
3.35-3.494.960.10615.29240.9950.119100
3.49-3.644.9980.08118.538840.9970.09199.8
3.64-3.824.8930.06622.268580.9980.07599.3
3.82-4.034.9620.05226.797960.9980.05899.4
4.03-4.274.8630.04131.067750.9990.046100
4.27-4.564.8850.03536.597230.9990.03999.4
4.56-4.934.8870.03240.116730.9990.036100
4.93-5.44.8280.03240.196350.9990.03698.8
5.4-6.044.8440.03438.115630.9990.03999.8
6.04-6.974.6710.02941.755010.9990.03399.4
6.97-8.544.6640.02150.643810.02399.5
8.54-12.084.5570.01559.6434310.01799.4
12.08-47.9573.8970.01754.81940.9990.0291.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX(1.14_3260)refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TS1

2ts1


Resolution: 2.7→47.957 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.62
RfactorNum. reflection% reflection
Rfree0.2903 1573 10.06 %
Rwork0.2257 --
obs0.2325 15636 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 183.56 Å2 / Biso mean: 78.8918 Å2 / Biso min: 32.7 Å2
Refinement stepCycle: final / Resolution: 2.7→47.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2732 0 0 30 2762
Biso mean---69.83 -
Num. residues----364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052787
X-RAY DIFFRACTIONf_angle_d0.7423770
X-RAY DIFFRACTIONf_dihedral_angle_d3.1491625
X-RAY DIFFRACTIONf_chiral_restr0.041416
X-RAY DIFFRACTIONf_plane_restr0.004484
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7001-2.78720.36031350.297112361371100
2.7872-2.88680.31281460.26312681414100
2.8868-3.00240.29561150.264412881403100
3.0024-3.1390.35671620.256312571419100
3.139-3.30450.29541640.232712211385100
3.3045-3.51150.33331120.233213011413100
3.5115-3.78250.34681260.221513071433100
3.7825-4.16290.32021280.214412911419100
4.1629-4.76480.22441400.190813021442100
4.7648-6.00140.26471580.217712831441100
6.0014-47.96480.28011870.23011309149699
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)
12.0703-0.01941.34292.921-0.31593.2742-0.0931-0.4568-0.42990.3054-0.0107-0.03420.0645-0.07650.10820.34710.066-00.49660.05780.8975-45.6618-20.673142.6285
21.76410.69661.82523.2435-0.44432.971-0.06490.7664-0.7339-0.2625-0.1838-0.6379-0.40780.59340.3670.27880.0393-0.13710.572-0.06750.8167-33.4429-13.264834.5125
34.30490.67292.45592.2316-1.83835.2892-0.36510.16570.50730.15070.0224-0.4252-0.48280.42580.3290.45070.0389-0.09370.3944-0.00110.948-34.6026-6.884637.0226
43.88660.3216-0.20062.9405-4.34366.4542-0.3726-0.7073-1.25-0.4958-0.4403-0.0211.36660.24750.21140.31680.0371-0.0340.89610.17081.5906-19.6557-27.800439.8858
54.13360.35590.86622.7010.76822.3195-0.0832-0.2574-0.6927-0.05690.0146-0.629-0.0980.44820.04750.41030.0509-0.06520.57340.16411.1064-31.4441-21.148643.8731
69.09680.8762-0.34252.4048-0.31967.7955-0.41760.50410.6951-0.1060.49740.00450.90820.0755-0.03340.5582-0.12080.23290.5554-0.09970.9057-46.6015-20.454220.1362
74.18122.3231-1.30067.3676-3.80094.7599-0.21920.3774-1.0308-0.01520.13350.24920.2626-0.520.06580.2494-0.01750.07920.5265-0.0680.67-60.7545-25.343728.4446
83.6253-3.89312.876.2898-2.29072.75660.02280.4666-0.0198-0.36150.13420.05570.4457-1.2181-0.22810.3985-0.10790.10260.87530.00420.5133-64.2716-11.96215.1358
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 59 )A1 - 59
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 89 )A60 - 89
3X-RAY DIFFRACTION3chain 'A' and (resid 90 through 138 )A90 - 138
4X-RAY DIFFRACTION4chain 'A' and (resid 139 through 168 )A139 - 168
5X-RAY DIFFRACTION5chain 'A' and (resid 169 through 229 )A169 - 229
6X-RAY DIFFRACTION6chain 'A' and (resid 230 through 252 )A230 - 252
7X-RAY DIFFRACTION7chain 'A' and (resid 253 through 312 )A253 - 312
8X-RAY DIFFRACTION8chain 'A' and (resid 313 through 345 )A313 - 345

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