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- PDB-7eiv: heterotetrameric glycyl-tRNA synthetase from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 7eiv
Titleheterotetrameric glycyl-tRNA synthetase from Escherichia coli
Components(Glycine--tRNA ligase ...) x 2
KeywordsLIGASE / Aminoacyl-tRNA synthetases class II
Function / homology
Function and homology information


glycine-tRNA ligase complex / arginine-tRNA ligase activity / arginyl-tRNA aminoacylation / glycyl-tRNA aminoacylation / glycine-tRNA ligase / glycine-tRNA ligase activity / ATP binding / cytosol
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / GLYCINE / Glycine--tRNA ligase alpha subunit / Glycine--tRNA ligase beta subunit
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.68 Å
AuthorsJu, Y. / Zhou, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81773636 China
National Natural Science Foundation of China (NSFC)81803435 China
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: X-shaped structure of bacterial heterotetrameric tRNA synthetase suggests cryptic prokaryote functions and a rationale for synthetase classifications.
Authors: Ju, Y. / Han, L. / Chen, B. / Luo, Z. / Gu, Q. / Xu, J. / Yang, X.L. / Schimmel, P. / Zhou, H.
History
DepositionMar 31, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)202,70412
Polymers201,4444
Non-polymers1,2608
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The apparent molecular weights of EcGlyRS575 in solution was measured using a HiLoad 16/60 Superdex 200 pg column (Cytiva) which was calibrated with standard proteins from ...Evidence: gel filtration, The apparent molecular weights of EcGlyRS575 in solution was measured using a HiLoad 16/60 Superdex 200 pg column (Cytiva) which was calibrated with standard proteins from Gel Filtration LMW Calibration Kit (Cytiva). The EcGlyRS575 was eluted at 64.6 mL with a MWSEC = 212.9 kDa, which is close to MWdeduced = 199.2 kDa and supports that EcGlyRS575 forms a heterotetramer in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15560 Å2
ΔGint-79 kcal/mol
Surface area69080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.371, 253.945, 270.738
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222

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Components

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Glycine--tRNA ligase ... , 2 types, 4 molecules ABCD

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


Mass: 35181.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: glyQ, glyS(A), b3560, JW3531 / Production host: Escherichia coli (E. coli) / References: UniProt: P00960, glycine-tRNA ligase
#2: Protein Glycine--tRNA ligase beta subunit / Glycyl-tRNA synthetase beta subunit / GlyRS


Mass: 65540.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: glyS, glyS(B), b3559, JW3530 / Production host: Escherichia coli (E. coli) / References: UniProt: P00961, glycine-tRNA ligase

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Non-polymers , 4 types, 64 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 4.47 Å3/Da / Density % sol: 72.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.4 M magnesium acetate, 0.1 M HEPES pH 6.8, 2% (v/v) PEG 3350, 2% (v/v) PEG 5000 MME, 2% (v/v) PEG 4000, 2% (v/v) PEG 2000 and 10% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.68→50 Å / Num. obs: 99458 / % possible obs: 100 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.024 / Rrim(I) all: 0.087 / Χ2: 2.02 / Net I/σ(I): 9.4 / Num. measured all: 1340079
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.68-2.7813.10.60298620.9630.1730.6270.466100
2.78-2.8913.90.43998960.9820.1210.4550.489100
2.89-3.0213.80.31198520.990.0860.3220.538100
3.02-3.1813.50.20799020.9940.0590.2160.638100
3.18-3.3813.20.13499060.9960.0380.140.838100
3.38-3.64140.09999400.9970.0270.1021.314100
3.64-413.50.07499070.9980.0210.0771.82100
4-4.5813.40.06299610.9980.0180.0652.877100
4.58-5.7713.40.064100340.9980.0180.0664.152100
5.77-5012.80.064101980.9980.0190.0667.2399.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.68→48.58 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.93 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.357 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2487 4996 5 %RANDOM
Rwork0.2282 ---
obs0.2293 94460 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 160.32 Å2 / Biso mean: 68.394 Å2 / Biso min: 39.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å2-0 Å2
2---4.98 Å20 Å2
3---5.15 Å2
Refinement stepCycle: final / Resolution: 2.68→48.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13251 0 76 56 13383
Biso mean--66.48 54 -
Num. residues----1701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01313643
X-RAY DIFFRACTIONr_bond_other_d0.0350.01712436
X-RAY DIFFRACTIONr_angle_refined_deg1.211.65318562
X-RAY DIFFRACTIONr_angle_other_deg2.2851.57328755
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5845.0061703
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.94622.369747
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.268152073
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9581596
X-RAY DIFFRACTIONr_chiral_restr0.0410.21771
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215513
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022905
LS refinement shellResolution: 2.68→2.747 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.347 358 -
Rwork0.336 6778 -
obs--97.69 %

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