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- PDB-7qcf: X-ray crystallographic structure of E. coli K-12 glycyl-tRNA synt... -

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Basic information

Entry
Database: PDB / ID: 7qcf
TitleX-ray crystallographic structure of E. coli K-12 glycyl-tRNA synthetase alpha subunit (glyQ)
ComponentsGlycine--tRNA ligase alpha subunit
KeywordsLIGASE / tRNA glycine
Function / homology
Function and homology information


glycine-tRNA ligase complex / glycyl-tRNA aminoacylation / glycine-tRNA ligase / glycine-tRNA ligase activity / ATP binding / cytosol
Similarity search - Function
Glycine-tRNA ligase, alpha subunit / Glycine-tRNA synthetase, heterodimeric / Glycyl-tRNA synthetase alpha subunit / Heterodimeric glycyl-transfer RNA synthetases family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
Similarity search - Domain/homology
Glycine--tRNA ligase alpha subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWeeks, S.D. / Munawar, A.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of E. coli K-12 glycyl-tRNA synthetase alpha subunit (glyQ)
Authors: Weeks, S.D. / Munawar, A.H.
History
DepositionNov 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycine--tRNA ligase alpha subunit
B: Glycine--tRNA ligase alpha subunit
C: Glycine--tRNA ligase alpha subunit
D: Glycine--tRNA ligase alpha subunit


Theoretical massNumber of molelcules
Total (without water)139,5054
Polymers139,5054
Non-polymers00
Water00
1
A: Glycine--tRNA ligase alpha subunit
B: Glycine--tRNA ligase alpha subunit


Theoretical massNumber of molelcules
Total (without water)69,7522
Polymers69,7522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Glycine--tRNA ligase alpha subunit

C: Glycine--tRNA ligase alpha subunit


Theoretical massNumber of molelcules
Total (without water)69,7522
Polymers69,7522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
3
D: Glycine--tRNA ligase alpha subunit

D: Glycine--tRNA ligase alpha subunit


Theoretical massNumber of molelcules
Total (without water)69,7522
Polymers69,7522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)232.407, 232.407, 123.577
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Glycine--tRNA ligase alpha subunit / Glycyl-tRNA synthetase alpha subunit / GlyRS


Mass: 34876.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: glyQ, glyS(A), b3560, JW3531 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00960, glycine-tRNA ligase

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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: 5.98 Å3/Da / Density % sol: 79.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM Morpheus buffer system 1, 0.5-3% w/v PEG 8000 and 20 % w/v ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9775 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 3→49.43 Å / Num. obs: 68043 / % possible obs: 100 % / Redundancy: 26.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.291 / Rpim(I) all: 0.057 / Rrim(I) all: 0.296 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3-3.0727.94.18312519444890.5130.8034.261.1100
14.07-49.3821.50.045161797540.9990.010.0463997.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSVERSION Feb 5, 2021data reduction
Aimless0.7.7data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F5W

5f5w


Resolution: 3→49.43 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.903 / SU B: 15.573 / SU ML: 0.265 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.365 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2579 2035 3 %RANDOM
Rwork0.2187 ---
obs0.2199 65933 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 237.19 Å2 / Biso mean: 89.276 Å2 / Biso min: 29.79 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å2-0 Å20 Å2
2---2.15 Å20 Å2
3---4.31 Å2
Refinement stepCycle: final / Resolution: 3→49.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9032 0 0 0 9032
Num. residues----1137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0129272
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.63812641
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.66651129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57423.092498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.192151430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7191545
X-RAY DIFFRACTIONr_chiral_restr0.1040.21181
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027225
LS refinement shellResolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 147 -
Rwork0.388 4797 -
all-4944 -
obs--99.96 %

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