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- PDB-5zdl: Crystal Structure Analysis of TtQRS in co-crystallised with ATP -

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Basic information

Entry
Database: PDB / ID: 5zdl
TitleCrystal Structure Analysis of TtQRS in co-crystallised with ATP
ComponentsGlutamine--tRNA ligase
KeywordsLIGASE / GlnRS / QRS / Synthetase
Function / homology
Function and homology information


glutamine-tRNA ligase / glutamine-tRNA ligase activity / glutaminyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / ATP binding / cytosol
Similarity search - Function
Glutamine-tRNA synthetase / : / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. ...Glutamine-tRNA synthetase / : / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / glutamine--tRNA ligase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsMutharasappan, N. / Jain, V. / Sharma, A. / Manickam, Y. / Jeyaraman, J.
CitationJournal: Int. J. Biol. Macromol. / Year: 2018
Title: Structural and functional analysis of Glutaminyl-tRNA synthetase (TtGlnRS) from Thermus thermophilus HB8 and its complexes
Authors: Nachiappan, M. / Jain, V. / Sharma, A. / Yogavel, M. / Jeyakanthan, J.
History
DepositionFeb 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: Glutamine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2086
Polymers63,5591
Non-polymers6495
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area23650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.084, 39.363, 114.846
Angle α, β, γ (deg.)90.000, 116.800, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glutamine--tRNA ligase


Mass: 63559.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HBB / Gene: TTHA0549 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SKU4, glutamine-tRNA ligase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl

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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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Ammonium sulfate, 0.1M Sodium cacodylate trihydrate pH 6.5, 30%(w/v) Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 0.976 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 18203 / % possible obs: 99.5 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.099 / Χ2: 1.775 / Net I/σ(I): 12.4 / Num. measured all: 102358
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.6-2.645.10.6578611.742197.4
2.64-2.695.30.6578891.6471100
2.69-2.745.40.5929061.6191100
2.74-2.85.40.4879351.62199.6
2.8-2.865.50.4338631.629199.2
2.86-2.935.50.3628971.5971100
2.93-35.50.3169411.5911100
3-3.085.60.2798731.639199.3
3.08-3.175.60.2489011.717199.9
3.17-3.285.60.1779361.789199.8
3.28-3.395.70.1598771.973199.7
3.39-3.535.70.1299221.81100
3.53-3.695.70.1079091.975199.9
3.69-3.885.70.0949241.933199.9
3.88-4.135.90.0789031.985199.4
4.13-4.455.80.0689372.024199.4
4.45-4.895.90.0589111.866199.7
4.89-5.660.0589281.706199.5
5.6-7.0560.0579191.741199.5
7.05-505.40.0529711.821197.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMACrefinement
HKL-2000data scaling
AMoREphasing
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QRU

1qru


Resolution: 2.6→46.19 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.894 / WRfactor Rfree: 0.2621 / WRfactor Rwork: 0.2016 / FOM work R set: 0.7656 / SU B: 31.934 / SU ML: 0.307 / SU R Cruickshank DPI: 0.345 / SU Rfree: 0.3992 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.399 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2868 1856 10.2 %RANDOM
Rwork0.2204 ---
obs0.2272 16346 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.99 Å2 / Biso mean: 49.234 Å2 / Biso min: 29.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å2-0 Å2-3.33 Å2
2--7.74 Å2-0 Å2
3----4.36 Å2
Refinement stepCycle: final / Resolution: 2.6→46.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4304 0 31 0 4335
Biso mean--47.09 --
Num. residues----539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194465
X-RAY DIFFRACTIONr_bond_other_d0.0010.024164
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9836088
X-RAY DIFFRACTIONr_angle_other_deg0.82339561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9755540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.34122.593216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1715703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6011547
X-RAY DIFFRACTIONr_chiral_restr0.080.2650
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215030
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021038
LS refinement shellResolution: 2.595→2.663 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 115 -
Rwork0.316 1110 -
all-1225 -
obs--91.83 %
Refinement TLS params.Method: refined / Origin x: 24.487 Å / Origin y: 0.35 Å / Origin z: 29.777 Å
111213212223313233
T0.0221 Å20.0059 Å20.0111 Å2-0.0502 Å2-0.0048 Å2--0.2804 Å2
L0.212 °20.0651 °20.4379 °2-0.2269 °2-0.068 °2--1.9315 °2
S-0.0096 Å °-0.0974 Å °0.048 Å °0.0304 Å °-0.0001 Å °0.0504 Å °-0.1712 Å °-0.2015 Å °0.0097 Å °

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