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- PDB-3rgl: The crystal structure of glycyl-tRNA synthetase subunit alpha fro... -

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Basic information

Entry
Database: PDB / ID: 3rgl
TitleThe crystal structure of glycyl-tRNA synthetase subunit alpha from Campylobacter jejuni subsp. jejuni NCTC in complex with ATP and glycine
ComponentsGlycyl-tRNA synthetase alpha subunit
KeywordsLIGASE / ALPHA/BETA PROTEIN / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID
Function / homology
Function and homology information


glycyl-tRNA aminoacylation / glycine-tRNA ligase / glycine-tRNA ligase activity / ATP binding / cytoplasm
Similarity search - Function
Class II aaRS and biotin synthetases; domain 2 / Glycine-tRNA ligase, alpha subunit / Glycine-tRNA synthetase, heterodimeric / Glycyl-tRNA synthetase alpha subunit / Heterodimeric glycyl-transfer RNA synthetases family profile. / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle ...Class II aaRS and biotin synthetases; domain 2 / Glycine-tRNA ligase, alpha subunit / Glycine-tRNA synthetase, heterodimeric / Glycyl-tRNA synthetase alpha subunit / Heterodimeric glycyl-transfer RNA synthetases family profile. / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / GLYCINE / (2S)-2-hydroxybutanedioic acid / Glycine--tRNA ligase alpha subunit
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsTan, K. / Zhang, R. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The crystal structure of glycyl-tRNA synthetase subunit alpha from Campylobacter jejuni subsp. jejuni NCTC in complex with ATP and glycine.
Authors: Tan, K. / Zhang, R. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionApr 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycyl-tRNA synthetase alpha subunit
B: Glycyl-tRNA synthetase alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7326
Polymers72,5082
Non-polymers1,2244
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-27 kcal/mol
Surface area22390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.740, 112.740, 157.753
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 36254.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: NCTC 11168 / Gene: Cj0704, glyQ / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q9PPK3, glycine-tRNA ligase
#2: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.66 Å3/Da / Density % sol: 53.78 %
Crystal growTemperature: 289 K / pH: 7
Details: 0.1M BIS-TRIS PROPANE:NAOH, 0.7M MAGNESIUM FORMATE, 10% Glycine, 10% ATP, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 24, 2011 / Details: MIRROR
RadiationMonochromator: SI 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.448→42 Å / Num. obs: 27496 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 22.5
Reflection shellResolution: 2.45→2.5 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 1.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RF1

3rf1


Resolution: 2.45→41.51 Å / SU ML: 0.31 / σ(F): 0 / Phase error: 26.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.233 1283 5.01 %
Rwork0.173 --
obs0.176 25633 93 %
all-25633 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.08 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.0048 Å2-0 Å2-0 Å2
2--8.0048 Å20 Å2
3----16.0096 Å2
Refinement stepCycle: LAST / Resolution: 2.45→41.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4698 0 76 13 4787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084898
X-RAY DIFFRACTIONf_angle_d1.1556652
X-RAY DIFFRACTIONf_dihedral_angle_d17.1071789
X-RAY DIFFRACTIONf_chiral_restr0.073681
X-RAY DIFFRACTIONf_plane_restr0.004857
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4482-2.54620.33381260.26082278X-RAY DIFFRACTION79
2.5462-2.66210.32431070.25022371X-RAY DIFFRACTION81
2.6621-2.80240.31751350.22392601X-RAY DIFFRACTION89
2.8024-2.97790.2581590.20562711X-RAY DIFFRACTION94
2.9779-3.20780.25341600.19212824X-RAY DIFFRACTION97
3.2078-3.53040.24351500.16672891X-RAY DIFFRACTION99
3.5304-4.04090.22411460.15532877X-RAY DIFFRACTION100
4.0409-5.08970.1821580.13792886X-RAY DIFFRACTION100
5.0897-41.51650.21831420.16882911X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -32.6397 Å / Origin y: 5.4596 Å / Origin z: 11.8428 Å
111213212223313233
T0.0543 Å20.0803 Å20.008 Å2-0.1217 Å2-0.0431 Å2--0.1251 Å2
L0.8131 °20.4063 °2-0.0318 °2-1.2382 °2-0.335 °2--2.4654 °2
S-0.0875 Å °0.0272 Å °0.0609 Å °0.0528 Å °0.1156 Å °0.0507 Å °-0.1513 Å °-0.1471 Å °0.004 Å °
Refinement TLS groupSelection details: ALL

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