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- PDB-3rf1: The crystal structure of glycyl-tRNA synthetase subunit alpha fro... -

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Basic information

Entry
Database: PDB / ID: 3rf1
TitleThe crystal structure of glycyl-tRNA synthetase subunit alpha from Campylobacter jejuni subsp. jejuni NCTC 11168
ComponentsGlycyl-tRNA synthetase alpha subunit
KeywordsLIGASE / glycyl-tRNA synthetase subunit alpha / 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 / cytosol
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
(2S)-2-hydroxybutanedioic acid / Glycine--tRNA ligase alpha subunit
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTan, K. / Zhang, R. / Zhou, M. / Hasseman, J. / 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 11168
Authors: Tan, K. / Zhang, R. / Zhou, M. / Hasseman, J. / Anderson, W.F. / Joachimiak, A.
History
DepositionApr 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 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)73,2379
Polymers72,5082
Non-polymers7297
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-26 kcal/mol
Surface area22020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.662, 112.662, 158.282
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: 81-176 / Gene: glyQ, CJJ81176_0727 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: A1VZ59, glycine-tRNA ligase
#2: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.67 Å3/Da / Density % sol: 53.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Bis-Tris Propane:NaOH, 0.7M Magnesium Formate, 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 Å
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: 2.2→39 Å / Num. all: 37970 / Num. obs: 37970 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 27.8
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1882 / % possible all: 99.8

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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 1J5W

1j5w


Resolution: 2.2→38.508 Å / SU ML: 0.27 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 1731 4.97 %random
Rwork0.1692 ---
all0.1715 34849 --
obs0.1715 34849 91.51 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.327 Å2 / ksol: 0.355 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.3088 Å2-0 Å2-0 Å2
2--9.3088 Å20 Å2
3----18.6175 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4690 0 48 45 4783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084853
X-RAY DIFFRACTIONf_angle_d1.036568
X-RAY DIFFRACTIONf_dihedral_angle_d15.4531772
X-RAY DIFFRACTIONf_chiral_restr0.071672
X-RAY DIFFRACTIONf_plane_restr0.004854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.27820.34051180.26242900X-RAY DIFFRACTION79
2.2782-2.36940.26861390.22932894X-RAY DIFFRACTION80
2.3694-2.47720.2611730.22233023X-RAY DIFFRACTION84
2.4772-2.60780.30291480.21133219X-RAY DIFFRACTION89
2.6078-2.77120.31471720.21613382X-RAY DIFFRACTION93
2.7712-2.9850.25711870.20553476X-RAY DIFFRACTION96
2.985-3.28530.25112120.19813486X-RAY DIFFRACTION98
3.2853-3.76030.21281920.16153625X-RAY DIFFRACTION100
3.7603-4.73630.16162060.13253579X-RAY DIFFRACTION100
4.7363-38.51370.18991840.14943534X-RAY DIFFRACTION98
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)
11.72580.3526-0.2931.13130.24142.81810.1208-0.39680.00250.0538-0.15420.06680.006-0.02510.02870.3688-0.0333-0.02970.42210.01290.335211.2683-36.6982-0.2357
21.539-0.0126-0.1050.57560.07342.6559-0.04550.2150.2182-0.42320.01040.0516-0.3996-0.03720.04250.59770.0255-0.05310.33750.09330.39212.0988-31.1309-23.3155
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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