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- PDB-7xof: Crystal structure of Oryza sativa plastid glycyl-tRNA synthetase -

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Basic information

Entry
Database: PDB / ID: 7xof
TitleCrystal structure of Oryza sativa plastid glycyl-tRNA synthetase
ComponentsGlycine--tRNA ligase
KeywordsLIGASE / Glycine-tRNA ligase / GlyRS / GlyRS2
Function / homology
Function and homology information


arginine-tRNA ligase activity / arginyl-tRNA aminoacylation / glycyl-tRNA aminoacylation / glycine-tRNA ligase / glycine-tRNA ligase activity / embryo development ending in seed dormancy / regulation of embryonic development / chloroplast / mitochondrion / ATP binding
Similarity search - Function
Glycine-tRNA ligase, beta subunit / Glycyl-tRNA synthetase beta subunit / Glycine-tRNA ligase, alpha subunit / Glycine-tRNA synthetase, heterodimeric / Glycyl-tRNA synthetase alpha subunit / Heterodimeric glycyl-transfer RNA synthetases family profile. / DALR anticodon binding / DALR anticodon binding domain / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
Similarity search - Domain/homology
glycine--tRNA ligase
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.56 Å
AuthorsYu, Z. / Lu, G. / Li, J.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32130063 China
National Natural Science Foundation of China (NSFC)31770784 China
Not funded2017YFA0504602
CitationJournal: To be published
Title: Crystal structure of Oryza sativa plastid glycyl-tRNA synthetase
Authors: Hao, Q. / Yu, Z. / Lu, G. / Lin, J.
History
DepositionMay 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycine--tRNA ligase
B: Glycine--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)234,1012
Polymers234,1012
Non-polymers00
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-19 kcal/mol
Surface area74070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.130, 130.940, 123.390
Angle α, β, γ (deg.)90.000, 101.880, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glycine--tRNA ligase


Mass: 117050.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: Os06g0103600, OsJ_19814, OSNPB_060103600 / Plasmid: pET26 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0DFB6, glycine-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.5 Å3/Da / Density % sol: 50.86 % / Mosaicity: 0 °
Crystal growTemperature: 289 K / Method: evaporation / pH: 7.5 / Details: PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.56→65.47 Å / Num. obs: 68702 / % possible obs: 93 % / Redundancy: 2.4 % / Biso Wilson estimate: 47.04 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.049 / Rrim(I) all: 0.083 / Net I/σ(I): 9.5 / Num. measured all: 168193 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.5 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.56-2.630.4671268151620.7860.3590.5922.194.8
11.45-65.470.02718587560.9980.020.03427.288.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F5W

5f5w


Resolution: 2.56→65.47 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2504 3383 4.93 %
Rwork0.21 65257 -
obs0.2119 68640 92.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 171.67 Å2 / Biso mean: 53.877 Å2 / Biso min: 23.92 Å2
Refinement stepCycle: final / Resolution: 2.56→65.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14584 0 0 218 14802
Biso mean---50.18 -
Num. residues----1851
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.56-2.60.34331610.33652727288895
2.6-2.640.37191490.32292821297095
2.64-2.680.34781390.30462764290395
2.68-2.720.3541330.2962756288994
2.72-2.770.31221350.28562748288394
2.77-2.820.36271340.26812756289094
2.82-2.870.3111740.26932708288293
2.87-2.930.29561260.26772723284992
2.93-2.990.31581590.26622740289994
2.99-3.060.34181480.24762728287694
3.06-3.140.31321590.25552747290694
3.14-3.230.25321390.23592735287493
3.23-3.320.26041520.22752703285593
3.32-3.430.25011410.21012710285192
3.43-3.550.25471250.21162729285492
3.55-3.690.25011290.2042696282591
3.69-3.860.25321390.1892731287092
3.86-4.060.22491250.18542714283992
4.06-4.320.20261470.17592686283391
4.32-4.650.22421250.16982710283591
4.65-5.120.21611130.16952665277890
5.12-5.860.22811530.19332672282591
5.86-7.380.22481510.20542636278789
7.38-65.470.16621270.1612652277988

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