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- PDB-5h4v: Structure of glutamyl-tRNA synthetase (Xoo1504) from Xanthomonas ... -

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Basic information

Entry
Database: PDB / ID: 5h4v
TitleStructure of glutamyl-tRNA synthetase (Xoo1504) from Xanthomonas oryzae pv. oryzae
ComponentsGlutamate--tRNA ligase
KeywordsLIGASE / Glutamyl-tRNA aminoacylation / ATP binding / Nucleotide binding
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-tRNA Synthetase; domain 2 / Glutamyl-trna Synthetase; Domain 2 / Glutamyl-tRNA Synthetase; domain 3 ...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-tRNA Synthetase; domain 2 / Glutamyl-trna Synthetase; Domain 2 / Glutamyl-tRNA Synthetase; domain 3 / Glutamyl-tRNA Synthetase; Domain 3 / 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. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glutamate--tRNA ligase
Similarity search - Component
Biological speciesXanthomonas oryzae pv. oryzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDoan, T.-N.-T. / Ho, T.-H. / Kang, L.-W.
CitationJournal: CROP PASTURE SCI / Year: 2017
Title: Transcriptional expression of aminoacyl tRNA synthetase genes of Xanthomonas oryzae pv. oryzae (Xoo) on rice-leaf extract treatment and crystal structure of Xoo glutamyl-tRNA synthetase
Authors: Ho, T.-H. / Hong, M.-K. / Kim, S. / Kim, J.-G. / Lee, J. / Jung, K. / Lee, I. / Choi, M. / Park, H. / Lee, S. / Ahn, Y.-J. / Kang, L.-W.
History
DepositionNov 2, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate--tRNA ligase
B: Glutamate--tRNA ligase
C: Glutamate--tRNA ligase
D: Glutamate--tRNA ligase
E: Glutamate--tRNA ligase
F: Glutamate--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)325,0896
Polymers325,0896
Non-polymers00
Water93752
1
A: Glutamate--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)54,1811
Polymers54,1811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutamate--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)54,1811
Polymers54,1811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glutamate--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)54,1811
Polymers54,1811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Glutamate--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)54,1811
Polymers54,1811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Glutamate--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)54,1811
Polymers54,1811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Glutamate--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)54,1811
Polymers54,1811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)186.353, 107.937, 165.895
Angle α, β, γ (deg.)90.00, 96.24, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Glutamate--tRNA ligase / Glutamyl-tRNA synthetase / GluRS


Mass: 54181.434 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85) (bacteria)
Strain: KACC10331 / KXO85 / Gene: gltX, XOO1504
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q5H2R3, glutamate-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.54 Å3/Da / Density % sol: 51.66 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 55%(v/v) Tacsimate, 0.1M bistris propane pH 6.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.96 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 4, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 59553 / % possible obs: 90.6 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.4
Reflection shellResolution: 3→3.11 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 1.8 / % possible all: 65.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CFO

2cfo


Resolution: 3→29.44 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.863 / SU B: 27.205 / SU ML: 0.478 / Cross valid method: THROUGHOUT / ESU R Free: 0.569 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.291 3046 5.1 %RANDOM
Rwork0.2 ---
obs0.204 56448 90.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å21.07 Å2
2---3.44 Å20 Å2
3---3.91 Å2
Refinement stepCycle: LAST / Resolution: 3→29.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21616 0 0 52 21668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01922050
X-RAY DIFFRACTIONr_bond_other_d0.0020.0221265
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.96429930
X-RAY DIFFRACTIONr_angle_other_deg1.085348734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.80352764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53723.8961037
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.612153683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.71415182
X-RAY DIFFRACTIONr_chiral_restr0.0910.23314
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02125224
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024990
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_it3.6767.00711089
X-RAY DIFFRACTIONr_mcbond_other3.6767.00711088
X-RAY DIFFRACTIONr_mcangle_it6.04510.50313842
X-RAY DIFFRACTIONr_mcangle_other6.04510.50313843
X-RAY DIFFRACTIONr_scbond_it3.1717.16910961
X-RAY DIFFRACTIONr_scbond_other3.1717.16910961
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.37210.64716088
X-RAY DIFFRACTIONr_long_range_B_refined9.02355.37425442
X-RAY DIFFRACTIONr_long_range_B_other9.02255.37525443
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.07 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 131 -
Rwork0.344 2719 -
obs--59.52 %

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