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- PDB-8jpv: Glutamyl-tRNA synthetase from Methylacidiphilum fumariolicum -

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Basic information

Entry
Database: PDB / ID: 8jpv
TitleGlutamyl-tRNA synthetase from Methylacidiphilum fumariolicum
ComponentsGlutamate--tRNA ligase
KeywordsLIGASE / catalytic activity
Function / homology
Function and homology information


glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / tRNA binding / zinc ion binding / ATP binding / cytosol
Similarity search - Function
Glutamate-tRNA ligase, bacterial/mitochondrial / Glutamyl-tRNA synthetase / Aminoacyl-tRNA synthetase, class I, anticodon-binding superfamily / Aminoacyl-tRNA synthetase, class I, anticodon-binding domain, subdomain 2 / Aminoacyl-tRNA synthetase, class I, anticodon-binding / Anticodon binding domain / : / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain ...Glutamate-tRNA ligase, bacterial/mitochondrial / Glutamyl-tRNA synthetase / Aminoacyl-tRNA synthetase, class I, anticodon-binding superfamily / Aminoacyl-tRNA synthetase, class I, anticodon-binding domain, subdomain 2 / Aminoacyl-tRNA synthetase, class I, anticodon-binding / Anticodon 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
Similarity search - Domain/homology
Glutamate--tRNA ligase
Similarity search - Component
Biological speciesMethylacidiphilum fumariolicum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsDev, A. / Basu, G.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India) India
CitationJournal: To Be Published
Title: Glutamyl-tRNA synthetase from Methylacidiphilum fumariolicum
Authors: Dev, A. / Basu, G.
History
DepositionJun 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)51,7931
Polymers51,7931
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.310, 62.540, 190.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glutamate--tRNA ligase


Mass: 51792.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylacidiphilum fumariolicum (bacteria)
Gene: gltX
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: I0JVL9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: HEPES buffer pH 7.0, 10% PEG 6000, 200 mM NaSCN

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS IV / Wavelength: 1.5419 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.51→95.14 Å / Num. obs: 16313 / % possible obs: 99.81 % / Redundancy: 6.2 % / CC1/2: 0.993 / Net I/σ(I): 9.5
Reflection shellResolution: 2.51→7.94 Å / Rmerge(I) obs: 0.161 / Num. unique obs: 17211

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→95.14 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.881 / SU B: 12.096 / SU ML: 0.256 / Cross valid method: THROUGHOUT / ESU R: 0.805 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26574 865 5 %RANDOM
Rwork0.20884 ---
obs0.21174 16313 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.303 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å20 Å2-0 Å2
2---1.2 Å20 Å2
3----0.55 Å2
Refinement stepCycle: 1 / Resolution: 2.51→95.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3539 0 0 127 3666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193638
X-RAY DIFFRACTIONr_bond_other_d0.0030.023479
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.964930
X-RAY DIFFRACTIONr_angle_other_deg1.01337995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5915443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04223.235170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.81115622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1861527
X-RAY DIFFRACTIONr_chiral_restr0.0740.2533
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214079
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02858
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5473.5811769
X-RAY DIFFRACTIONr_mcbond_other2.5473.581768
X-RAY DIFFRACTIONr_mcangle_it4.1445.3662213
X-RAY DIFFRACTIONr_mcangle_other4.1445.3682214
X-RAY DIFFRACTIONr_scbond_it2.5213.7781869
X-RAY DIFFRACTIONr_scbond_other2.5213.7731867
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1865.5652717
X-RAY DIFFRACTIONr_long_range_B_refined7.79533.41215536
X-RAY DIFFRACTIONr_long_range_B_other7.79433.4215512
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.511→2.576 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 62 -
Rwork0.297 1183 -
obs--100 %

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