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- PDB-3tze: Crystal structure of a tryptophanyl-tRNA synthetase from Encephal... -

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Basic information

Entry
Database: PDB / ID: 3tze
TitleCrystal structure of a tryptophanyl-tRNA synthetase from Encephalitozoon cuniculi bound to tryptophan
ComponentsTryptophanyl-tRNA synthetase
KeywordsLIGASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / amino acylation / eukaryotic pathogen / Microsporidia / Fungi / intracellular parasite
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / ATP binding
Similarity search - Function
Tryptophan-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold ...Tryptophan-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / TRYPTOPHAN / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesEncephalitozoon cuniculi (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Sci Rep / Year: 2017
Title: Ligand co-crystallization of aminoacyl-tRNA synthetases from infectious disease organisms.
Authors: Moen, S.O. / Edwards, T.E. / Dranow, D.M. / Clifton, M.C. / Sankaran, B. / Van Voorhis, W.C. / Sharma, A. / Manoil, C. / Staker, B.L. / Myler, P.J. / Lorimer, D.D.
History
DepositionSep 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Sep 13, 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 / struct_ref_seq_dif / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tryptophanyl-tRNA synthetase
B: Tryptophanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,6296
Polymers93,1422
Non-polymers4874
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-25 kcal/mol
Surface area27630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.110, 79.160, 177.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 46571.125 Da / Num. of mol.: 2 / Mutation: A149T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Encephalitozoon cuniculi (fungus) / Strain: GB-M1 / Gene: ECU11_0530 / Production host: Escherichia coli (E. coli) / References: UniProt: O96771, tryptophan-tRNA ligase
#2: Chemical ChemComp-TRP / TRYPTOPHAN


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


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.04 Å3/Da / Density % sol: 39.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: EncuA.00600.a.A1 PS00344 at 23.5 mg/mL against Wizard III screen from Emerald BioSystems, 20% PEG 3350, 0.2 M potassium nitrate, crystal tracking ID 221699a8, pH 7, VAPOR DIFFUSION, SITTING ...Details: EncuA.00600.a.A1 PS00344 at 23.5 mg/mL against Wizard III screen from Emerald BioSystems, 20% PEG 3350, 0.2 M potassium nitrate, crystal tracking ID 221699a8, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorDetector: CCD / Date: Sep 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 24185 / Num. obs: 23335 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 48.833 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 14.71
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.6-2.673.40.5172.2353891760157589.5
2.67-2.740.4212.875738156089.6
2.74-2.820.3813.315851152292
2.82-2.910.314.236149149993.5
2.91-30.2664.946518151295.1
3-3.110.2386.066742144996.9
3.11-3.230.1868.026882143897.9
3.23-3.360.15510.097136141499
3.36-3.510.11213.937016133099
3.51-3.680.09217.616890130198.9
3.68-3.880.07521.056747125499.1
3.88-4.110.06523.76413117499.2
4.11-4.390.05427.125966109499.4
4.39-4.750.04929.015741104799.5
4.75-5.20.04629.04535596399.8
5.2-5.810.0526.65496988699.9
5.81-6.710.04926.12442679299.6
6.71-8.220.03631.53367666599.7
8.22-11.630.02739.46287653999.6
11.63-500.02536.17155432198.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å46.17 Å
Translation3 Å46.17 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ULH

1ulh


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.2232 / WRfactor Rwork: 0.1837 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8337 / SU B: 22.715 / SU ML: 0.234 / SU R Cruickshank DPI: 2.5214 / SU Rfree: 0.3291 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 1191 5.1 %RANDOM
Rwork0.2021 ---
obs0.2044 23335 96.48 %-
all-24185 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.86 Å2 / Biso mean: 43.2257 Å2 / Biso min: 23.67 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å20 Å20 Å2
2---0.12 Å20 Å2
3---1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5379 0 32 61 5472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.025531
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.9547497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46123.876258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.82115853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0441530
X-RAY DIFFRACTIONr_chiral_restr0.0980.2824
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214279
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 81 -
Rwork0.271 1389 -
all-1470 -
obs--88.77 %
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)
10.70360.6403-0.18450.9049-0.80932.2646-0.0466-0.1148-0.0086-0.0365-0.10650.0390.12880.28330.15310.1513-0.03010.0080.13210.04880.192530.437629.8745-28.4904
20.6920.61561.05770.55850.92031.67250.0504-0.0540.01180.0842-0.0513-0.00010.0033-0.04410.00090.15220.0067-0.00070.1217-0.00320.204813.84529.8649-37.8436
30.875-0.4031.1460.2904-0.19872.57160.1223-0.1772-0.178-0.01290.11410.09280.2909-0.252-0.23640.2259-0.1251-0.04540.19270.0520.247125.705326.1428-35.5558
41.28860.18310.71770.2578-0.52072.07670.1546-0.1717-0.06850.0488-0.07360.01320.01480.0231-0.0810.1765-0.0396-0.01710.1472-0.00980.12723.010622.4676-11.4547
51.4734-0.13120.07050.2055-0.39170.88230.0828-0.0823-0.0706-0.0681-0.00980.02550.0151-0.0676-0.0730.16270.0292-0.00190.1447-0.00250.1995-13.567425.9902-68.4021
60.6242-0.11520.5770.0382-0.11510.5410.03810.0020.0488-0.0057-0.04810.00980.02520.01760.010.15010.01140.010.13280.00280.2309-0.778428.2422-57.8335
71.66570.68680.40883.07871.13811.1589-0.195-0.06130.0137-0.62560.1159-0.1915-0.074-0.11690.07910.3071-0.00320.08610.08140.0020.1018-7.293634.9629-88.2229
81.3207-2.22241.85685.6719-3.63562.8035-0.23170.10350.3010.6012-0.0873-0.3967-0.40610.05330.31890.1830.0544-0.04930.10460.0360.3041-5.875748.2485-64.6638
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 104
2X-RAY DIFFRACTION2A105 - 218
3X-RAY DIFFRACTION3A219 - 272
4X-RAY DIFFRACTION4A273 - 384
5X-RAY DIFFRACTION5B24 - 111
6X-RAY DIFFRACTION6B112 - 263
7X-RAY DIFFRACTION7B264 - 362
8X-RAY DIFFRACTION8B363 - 383

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