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- PDB-6mtk: Crystal structure of Tryptophanyl-tRNA synthetase from Elizabethk... -

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Basic information

Entry
Database: PDB / ID: 6mtk
TitleCrystal structure of Tryptophanyl-tRNA synthetase from Elizabethkingia anophelis NUHP1
ComponentsTryptophanyl-tRNA synthetase
KeywordsLIGASE / SSGCID / Structural Genomics / Elizabethkingia anophelis / BD94_0195 / Tryptophanyl-tRNA synthetase / 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
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) / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...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
Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesElizabethkingia anophelis NUHP1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of Tryptophanyl-tRNA synthetase from Elizabethkingia anophelis NUHP1
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionOct 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Refinement description / Category: refine_ls_restr
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: Tryptophanyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)37,5011
Polymers37,5011
Non-polymers00
Water2,216123
1
A: Tryptophanyl-tRNA synthetase

A: Tryptophanyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)75,0022
Polymers75,0022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area3480 Å2
ΔGint-27 kcal/mol
Surface area26720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.070, 105.920, 94.190
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-473-

HOH

21A-499-

HOH

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Components

#1: Protein Tryptophanyl-tRNA synthetase


Mass: 37500.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia anophelis NUHP1 (bacteria)
Gene: BD94_0195 / Plasmid: ElanA.00743.a.B1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: A0A077EER2, tryptophan-tRNA ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.17 Å3/Da / Density % sol: 43.3 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 22.6 mg/mL ElanA.00743.a.B1.PS38400 + Molecular Dimensions Morpheus screen, condition C10 (10% w/v PEG8000, 20% v/v ethylene glycol, 30 mM each NPS, 100 mM bicine/Trizma base, pH 8.5, sodium ...Details: 22.6 mg/mL ElanA.00743.a.B1.PS38400 + Molecular Dimensions Morpheus screen, condition C10 (10% w/v PEG8000, 20% v/v ethylene glycol, 30 mM each NPS, 100 mM bicine/Trizma base, pH 8.5, sodium nitrate, 0.3 M disodium hydrogen phosphate, 0.3 M ammonium sulfate), cryoprotectant: direct, Tray 299155c10, puck OVZ1-7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 14, 2018
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→47.095 Å / Num. obs: 22221 / % possible obs: 99.3 % / Redundancy: 12.517 % / Biso Wilson estimate: 45.669 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.043 / Χ2: 1.031 / Net I/σ(I): 33.22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.058.3630.5074.1916430.950.5499.9
2.05-2.119.250.3925.7915640.970.41699.7
2.11-2.1710.0960.3047.9215610.9840.32199.7
2.17-2.2410.6060.25110.0214770.9880.26399.3
2.24-2.3111.1910.19412.3214530.9960.20398.9
2.31-2.3912.0150.16315.1114020.9960.17199.2
2.39-2.4813.710.13518.8713460.9980.1498.5
2.48-2.5814.4130.1123.4912920.9990.11498.6
2.58-2.714.4170.09526.6712530.9990.09998.7
2.7-2.8314.4430.07532.5512000.9990.07898.8
2.83-2.9814.4260.06337.8811220.9990.06698.5
2.98-3.1614.3850.05344.9410990.9990.05599.9
3.16-3.3814.270.0456.96102810.04299.8
3.38-3.6514.230.03566.2197010.03799.9
3.65-414.020.03176.1188010.03399.5
4-4.4713.9360.02882.0681510.02999.9
4.47-5.1614.150.02684.6971510.02799.9
5.16-6.3213.8240.02682.3262410.02799.8
6.32-8.9413.5030.02486.6848910.025100
8.94-47.09511.8540.02686.962880.9990.02799

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
MoRDaphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3TZL as per MoRDa

3tzl


Resolution: 2→47.095 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.03
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 1936 8.72 %0
Rwork0.1998 ---
obs0.204 22197 99.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 115.07 Å2 / Biso mean: 50.5227 Å2 / Biso min: 23.75 Å2
Refinement stepCycle: final / Resolution: 2→47.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2394 0 0 126 2520
Biso mean---48.05 -
Num. residues----311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062461
X-RAY DIFFRACTIONf_angle_d0.7683347
X-RAY DIFFRACTIONf_dihedral_angle_d13.0681490
X-RAY DIFFRACTIONf_chiral_restr0.047388
X-RAY DIFFRACTIONf_plane_restr0.005435
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 (%)
2.0001-2.05010.35791180.273714661584100
2.0501-2.10550.3171980.26114451543100
2.1055-2.16750.31341300.249714571587100
2.1675-2.23740.27021430.23481408155199
2.2374-2.31740.33041230.23981452157599
2.3174-2.41020.3421220.25051438156099
2.4102-2.51990.29521280.23891418154698
2.5199-2.65270.30621350.25721412154798
2.6527-2.81890.33241600.23481427158799
2.8189-3.03650.30731530.23881427158099
3.0365-3.3420.25121530.217714261579100
3.342-3.82540.22721640.178714681632100
3.8254-4.81880.21221320.153514861618100
4.8188-47.1080.18571770.168815311708100
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)
10.4006-0.52880.29316.7519-1.62811.27860.1519-0.009-0.1207-0.4041-0.2578-0.20510.3056-0.10290.12140.3098-0.05790.01830.31970.00190.266821.725337.4725-0.0774
2-0.8435-0.1968-0.32067.0505-6.35515.9969-0.01080.0769-0.0261-0.01110.29470.3513-0.1212-0.5251-0.38080.456-0.069-0.050.48810.02260.414815.827830.11510.8111
30.5497-0.4292-0.07115.0555-2.08192.36470.0984-0.0043-0.12390.2346-0.3349-0.45610.11040.10450.17760.2645-0.0269-0.03080.2862-0.03350.247323.370318.25168.301
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 145 )A0 - 145
2X-RAY DIFFRACTION2chain 'A' and (resid 146 through 214 )A146 - 214
3X-RAY DIFFRACTION3chain 'A' and (resid 215 through 321 )A215 - 321

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