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- PDB-2q5h: Crystal structure of apo-wildtype Glycyl-tRNA synthetase -

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Basic information

Entry
Database: PDB / ID: 2q5h
TitleCrystal structure of apo-wildtype Glycyl-tRNA synthetase
ComponentsGlycyl-tRNA synthetaseGlycine—tRNA ligase
KeywordsLIGASE / Aminoacyl-tRNA synthetase / ATP-binding / Structural Genomics / Glycyl-tRNA Synthetase / Oxford Protein Production Facility / OPPF
Function / homology
Function and homology information


mitochondrial glycyl-tRNA aminoacylation / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / glycine-tRNA ligase / glycine-tRNA ligase activity / Mitochondrial tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / secretory granule / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases ...mitochondrial glycyl-tRNA aminoacylation / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / glycine-tRNA ligase / glycine-tRNA ligase activity / Mitochondrial tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / secretory granule / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / protein dimerization activity / mitochondrial matrix / axon / mitochondrion / extracellular exosome / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Herpes Virus-1 - #230 / Glycyl-tRNA synthetase / Glycyl-tRNA synthetase-like core domain / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Anticodon-binding domain ...Herpes Virus-1 - #230 / Glycyl-tRNA synthetase / Glycyl-tRNA synthetase-like core domain / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Anticodon-binding domain / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Herpes Virus-1 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / S15/NS1, RNA-binding / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glycine--tRNA ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCader, M.Z. / Ren, J. / James, P.A. / Bird, L.E. / Talbot, K. / Stammers, D.K. / Oxford Protein Production Facility (OPPF)
CitationJournal: Febs Lett. / Year: 2007
Title: Crystal structure of human wildtype and S581L-mutant glycyl-tRNA synthetase, an enzyme underlying distal spinal muscular atrophy.
Authors: Cader, M.Z. / Ren, J. / James, P.A. / Bird, L.E. / Talbot, K. / Stammers, D.K.
History
DepositionJun 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)78,4631
Polymers78,4631
Non-polymers00
Water18010
1
A: Glycyl-tRNA synthetase

A: Glycyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)156,9252
Polymers156,9252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_644y+1,x-1,-z-11
Buried area5510 Å2
ΔGint-40 kcal/mol
Surface area46740 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.530, 92.530, 246.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is a homodimer generated from the monomer in the asymmetric unit by the symmetry operation Y,X,-Z

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Components

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


Mass: 78462.555 Da / Num. of mol.: 1 / Fragment: Residues 55-739
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GARS / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41250, glycine-tRNA ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.37 Å3/Da / Density % sol: 63.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 3350, 0.2M Sodium bromide, 0.1M Bis-Tris propane, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 23, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 21172 / % possible obs: 95.6 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.186 / Net I/σ(I): 10.3
Reflection shellResolution: 3→3.11 Å / Redundancy: 8 % / Rmerge(I) obs: 0.986 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1941 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ATI

1ati


Resolution: 3→29.27 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.904 / SU B: 32.662 / SU ML: 0.263 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.734 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. O program has also been used in structure solution. CNS program has also been used in the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.25013 1021 4.8 %RANDOM
Rwork0.20526 ---
obs0.20749 20082 94.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.316 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 3→29.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4213 0 0 10 4223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224310
X-RAY DIFFRACTIONr_bond_other_d0.0010.022978
X-RAY DIFFRACTIONr_angle_refined_deg1.0041.9525823
X-RAY DIFFRACTIONr_angle_other_deg0.77337224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7225525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57923.897213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.34715741
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7131530
X-RAY DIFFRACTIONr_chiral_restr0.0580.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024808
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02910
X-RAY DIFFRACTIONr_nbd_refined0.2160.2942
X-RAY DIFFRACTIONr_nbd_other0.1810.22986
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22127
X-RAY DIFFRACTIONr_nbtor_other0.0820.22372
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.288
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1850.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0840.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.87743413
X-RAY DIFFRACTIONr_mcbond_other0.55541064
X-RAY DIFFRACTIONr_mcangle_it3.96664247
X-RAY DIFFRACTIONr_scbond_it5.09561958
X-RAY DIFFRACTIONr_scangle_it7.564121576
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 44 -
Rwork0.326 1182 -
obs--76.87 %
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)
12.4704-0.03750.63631.6798-0.43951.9873-0.08920.45690.368-0.27510.0693-0.0565-0.37410.1160.0199-0.15310.0251-0.0367-0.24730.1053-0.231383.22217.2475-134.5053
24.4334-4.43472.75039.4291-2.05041.8046-0.1797-0.48960.1460.74350.19750.0166-0.6172-0.3193-0.01790.3355-0.0452-0.01930.04250.05620.313986.976936.2537-128.735
35.03470.7591-1.37137.314-2.45473.4994-0.0838-0.5856-0.29320.47860.18250.395-0.0694-0.4138-0.0987-0.31390.11340.0480.00040.1177-0.261563.0129-9.1464-108.6475
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA64 - 14364 - 143
2X-RAY DIFFRACTION1AA226 - 538226 - 538
3X-RAY DIFFRACTION2AA144 - 225144 - 225
4X-RAY DIFFRACTION3AA539 - 673539 - 673

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