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- PDB-3foc: Tryptophanyl-tRNA synthetase from Giardia lamblia -

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Basic information

Entry
Database: PDB / ID: 3foc
TitleTryptophanyl-tRNA synthetase from Giardia lamblia
ComponentsTryptophanyl-tRNA synthetase
KeywordsLIGASE / STRUCTURAL GENOMICS / tryptophanyl-tRNA synthetase / giardiasis / Aminoacyl-tRNA synthetase / Medical Structural Genomics of Pathogenic Protozoa / MSGPP
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophanyl-tRNA aminoacylation / tryptophan-tRNA ligase activity / ATP binding / cytoplasm
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--tRNA ligase
Similarity search - Component
Biological speciesGiardia lamblia ATCC 50803 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 Å
AuthorsArakaki, T.L. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP)
Citation
Journal: J.Struct.Biol. / Year: 2010
Title: The structure of tryptophanyl-tRNA synthetase from Giardia lamblia reveals divergence from eukaryotic homologs.
Authors: Arakaki, T.L. / Carter, M. / Napuli, A.J. / Verlinde, C.L. / Fan, E. / Zucker, F. / Buckner, F.S. / Van Voorhis, W.C. / Hol, W.G. / Merritt, E.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Optimal description of a protein structure in terms of multiple groups undergoing TLS motion.
Authors: Painter, J. / Merritt, E.A.
History
DepositionDec 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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 / 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 / _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)101,7285
Polymers101,4432
Non-polymers2843
Water6,575365
1
A: Tryptophanyl-tRNA synthetase
B: Tryptophanyl-tRNA synthetase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)203,45510
Polymers202,8874
Non-polymers5686
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area14480 Å2
ΔGint-83.5 kcal/mol
Surface area61470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.714, 140.147, 90.352
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Tryptophanyl-tRNA synthetase


Mass: 50721.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Gint003032AAA, GiardiaDB GL50803_3032 / Source: (gene. exp.) Giardia lamblia ATCC 50803 (eukaryote) / Gene: GL50803_3032 / Plasmid: AVA421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8B8N3, tryptophan-tRNA ligase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THERE IS A THREONINE AT POSITION 384 AS DETERMINED BY SEQUENCING. THIS CONFLICT ...AUTHORS STATE THAT THERE IS A THREONINE AT POSITION 384 AS DETERMINED BY SEQUENCING. THIS CONFLICT MAY BE DUE TO STRAIN VARIATION.

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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: 3.33 Å3/Da / Density % sol: 63.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.2
Details: 2.7 M (NH4)2SO4, 0.1 M Citric acid pH 5.2, 5mM DTT, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionRedundancy: 6.2 % / Av σ(I) over netI: 20.92 / Number: 200381 / Rmerge(I) obs: 0.127 / Χ2: 0.99 / D res high: 2.8 Å / D res low: 40 Å / Num. obs: 32421 / % possible obs: 93.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.034010010.0680.9957
4.796.0399.810.1010.9816.9
4.184.7999.910.121.0947.1
3.84.1899.910.1490.9397.2
3.533.899.910.2191.0317.2
3.323.5310010.2350.9966.9
3.153.3299.910.28216.2
3.023.1596.810.3470.9054.9
2.93.0281.710.4440.8643.6
2.82.956.510.480.8332.4
ReflectionResolution: 2.09→40 Å / Num. obs: 77780 / % possible obs: 97.3 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.089 / Χ2: 1.021 / Net I/σ(I): 20.921
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.09-2.185.10.6164550.909182
2.18-2.265.80.45273340.988192.6
2.26-2.376.30.39377381.022198.2
2.37-2.496.90.29779031.048199.7
2.49-2.657.30.22879381.0191100
2.65-2.857.40.16179440.9511100
2.85-3.147.50.1279920.9651100
3.14-3.597.50.09580181.0411100
3.59-4.527.40.07880921.0881100
4.52-407.20.05183661.113199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.19 Å38.91 Å
Translation3.19 Å38.91 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2IP1

2ip1


Resolution: 2.09→40 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.252 / WRfactor Rwork: 0.214 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.84 / SU B: 9.773 / SU ML: 0.114 / SU R Cruickshank DPI: 0.17 / SU Rfree: 0.158 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.234 3910 5 %RANDOM
Rwork0.199 ---
obs0.2 77712 96.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 90.49 Å2 / Biso mean: 28.296 Å2 / Biso min: 10.43 Å2
Baniso -1Baniso -2Baniso -3
1-3.84 Å20 Å20 Å2
2---2.65 Å20 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 2.09→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6371 0 16 365 6752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226688
X-RAY DIFFRACTIONr_bond_other_d0.0010.024679
X-RAY DIFFRACTIONr_angle_refined_deg1.0031.9769069
X-RAY DIFFRACTIONr_angle_other_deg0.788311362
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5325840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.30723310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.77151157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.341552
X-RAY DIFFRACTIONr_chiral_restr0.0610.2990
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217439
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021453
X-RAY DIFFRACTIONr_mcbond_it0.451.54067
X-RAY DIFFRACTIONr_mcbond_other0.0691.51635
X-RAY DIFFRACTIONr_mcangle_it0.85326578
X-RAY DIFFRACTIONr_scbond_it1.17132621
X-RAY DIFFRACTIONr_scangle_it1.9734.52471
LS refinement shellResolution: 2.09→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 240 -
Rwork0.284 4031 -
all-4271 -
obs--72.75 %
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)
18.83660.283.13280.9817-0.32131.3011-0.1274-0.05010.1469-0.04690.10450.1225-0.0403-0.10440.02290.17770.04180.03880.2308-0.05980.15487.734334.525473.0015
20.2567-0.1401-0.15792.0397-0.21240.8119-0.02810.0393-0.0151-0.0330.03420.03070.1715-0.128-0.00610.1786-0.02010.00310.2063-0.0090.192622.650114.818671.3697
36.503-1.75-0.79834.5945-0.29564.7194-0.05580.43110.225-0.33540.12870.52390.1507-1.1931-0.07290.1353-0.1124-0.05560.38560.0560.094112.435233.09345.1878
41.54-1.04070.06192.8475-1.66282.3619-0.01550.06760.2392-0.06650.0801-0.1964-0.0708-0.2605-0.06460.1388-0.05320.03550.2132-0.00040.210924.642532.717755.5344
56.6109-1.51812.11861.4876-0.33950.8606-0.18480.1140.183-0.04120.1027-0.0571-0.20450.19190.08220.1811-0.0590.03530.23720.0370.1631-4.00635.57563.3184
60.81740.17970.18571.37940.86852.0626-0.0257-0.04320.1337-0.00660.11530.0180.02360.0977-0.08960.12130.0012-0.00870.20040.0060.2308-18.348331.38468.3216
70.22650.2793-0.13591.7461-0.00491.1275-0.03370.0145-0.025-0.05640.0276-0.14380.23860.0930.00610.1836-0.0081-0.01040.19170.00860.1886-20.83714.606566.1148
81.66420.84420.09182.16111.10522.42720.002-0.08350.11170.13440.2222-0.28-0.03290.5059-0.22410.10380.02390.01490.2388-0.07710.2153-14.150436.383986.0619
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 35
2X-RAY DIFFRACTION2A36 - 303
3X-RAY DIFFRACTION3A304 - 356
4X-RAY DIFFRACTION4A357 - 429
5X-RAY DIFFRACTION5B3 - 39
6X-RAY DIFFRACTION6B40 - 103
7X-RAY DIFFRACTION7B104 - 300
8X-RAY DIFFRACTION8B301 - 429

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