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

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Basic information

Entry
Database: PDB / ID: 3ufg
TitleThe crystal structure of glycyl-tRNA synthetase subunit alpha from Campylobacter jejuni subsp. jejuni NCTC in complex with ATP
ComponentsGlycyl-tRNA synthetase alpha subunit
KeywordsLIGASE / 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 / LEUCINE / Glycine--tRNA ligase alpha subunit
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.552 Å
AuthorsTan, K. / Zhou, M. / Peterson, S. / 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
Authors: Tan, K. / Zhou, M. / Peterson, S. / Anderson, W.F. / Joachimiak, A.
History
DepositionNov 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 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 1.2Dec 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)73,6545
Polymers72,5082
Non-polymers1,1463
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-24 kcal/mol
Surface area22220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.580, 114.580, 157.707
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) / Gene: glyQ, Cj0704 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) majic / References: UniProt: Q9PPK3, glycine-tRNA ligase
#2: 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
#3: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2

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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: 2.75 Å3/Da / Density % sol: 55.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.3M Magnesium Format, 0.1M Tris:HCl, pH 8.5, 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: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 24, 2011 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.55→42 Å / Num. all: 24077 / Num. obs: 24077 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 23.3
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 1.3 / Num. unique all: 1214 / % possible all: 98.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RF1

3rf1


Resolution: 2.552→41.994 Å / SU ML: 0.83 / σ(F): 1.96 / Phase error: 33.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2551 1203 5.03 %Random
Rwork0.1736 ---
obs0.1776 23924 95.31 %-
all-23924 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 81.028 Å2 / ksol: 0.355 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.2123 Å20 Å2-0 Å2
2--15.2123 Å20 Å2
3----30.4246 Å2
Refinement stepCycle: LAST / Resolution: 2.552→41.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4698 0 71 0 4769
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074894
X-RAY DIFFRACTIONf_angle_d1.0696648
X-RAY DIFFRACTIONf_dihedral_angle_d16.9761788
X-RAY DIFFRACTIONf_chiral_restr0.069683
X-RAY DIFFRACTIONf_plane_restr0.004855
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.552-2.65450.41511400.34142565X-RAY DIFFRACTION97
2.6545-2.77530.34851530.29662590X-RAY DIFFRACTION99
2.7753-2.92150.36111420.25312626X-RAY DIFFRACTION99
2.9215-3.10450.34261370.23372648X-RAY DIFFRACTION99
3.1045-3.34410.30991290.20972627X-RAY DIFFRACTION99
3.3441-3.68050.21111490.15862612X-RAY DIFFRACTION99
3.6805-4.21260.24491160.13792432X-RAY DIFFRACTION91
4.2126-5.30580.19961030.12882170X-RAY DIFFRACTION82
5.3058-41.99930.23471340.16282451X-RAY DIFFRACTION92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.06220.8457-1.41571.98920.75093.2449-0.119-0.2918-0.4481-0.05560.1220.07320.04180.3132-0.04360.74970.10970.06650.5144-0.03450.495527.651719.3842-3.7718
23.67323.1417-0.96986.8228-1.21174.9547-0.0445-0.21480.19861.0625-0.0399-0.0478-0.55520.57550.03660.76030.1355-0.1080.6921-0.06070.658532.639532.7821-2.6408
36.8693-2.0483-0.40812.79770.12822.4227-0.3847-1.107-0.29240.55960.6494-0.15480.33210.9458-0.25470.96550.1103-0.04430.8584-0.02440.594829.820120.2528.2395
40.802-1.5111-0.88493.05550.84734.8229-0.3286-0.6580.3970.45440.32570.06480.1470.6215-0.00020.85760.0368-0.01370.8384-0.04290.705128.876123.79266.8818
52.2536-1.6420.61658.9689-0.66222.47280.13490.4583-0.1558-0.1674-0.1896-0.59240.21240.8480.03610.61850.0281-0.02451.0711-0.01610.675341.78731.316-11.0194
67.67932.587-0.4926.0923-0.75723.6776-0.1806-0.41120.54590.64170.22860.3102-0.7117-0.59480.00370.8060.18930.03830.7841-0.04510.571415.795743.3605-5.3531
76.76134.5306-0.12523.5451.60325.33830.1457-0.22660.21290.79620.12850.2678-0.1993-0.0963-0.2470.86910.3007-0.0010.7859-0.01560.622410.894738.36823.798
84.507-0.6789-1.10783.71220.18365.3229-0.20310.6432-0.3580.1957-0.02090.31530.5922-0.18720.23310.6450.0099-0.05910.7054-0.15470.587925.402822.3017-20.9806
92.39150.4026-0.73016.2226-2.39623.9812-0.27410.7022-0.3317-0.87760.20930.27640.8078-0.39610.06950.8398-0.0578-0.12490.9627-0.24610.686924.385218.0401-31.9531
102.4034-1.78470.46963.8019-0.20113.49520.02050.0376-0.71280.4191-0.05440.78690.7202-0.6653-0.08460.7404-0.39240.05850.8899-0.13891.05559.310117.1048-12.6231
119.16451.2726-3.01922.6395-0.6333.1535-0.21960.50640.3714-0.11820.25210.2434-0.665-0.4915-0.04190.84730.0424-0.08950.7473-0.0030.555920.889543.8262-22.8118
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ -7:47)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 48:72)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 73:129)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 130:168)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 169:206)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 207:257)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 258:284)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ -1:86)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 87:168)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 169:206)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 207:284)

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