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- PDB-1b76: GLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH ATP -

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Basic information

Entry
Database: PDB / ID: 1b76
TitleGLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH ATP
ComponentsGlycine--tRNA ligase
KeywordsLIGASE / AMINOACYL-TRNA SYNTHASE / LIGASE(SYNTHETASE)
Function / homology
Function and homology information


glycine-tRNA ligase complex / glycyl-tRNA aminoacylation / glycine-tRNA ligase / glycine-tRNA ligase activity / glycine binding / protein dimerization activity / magnesium ion binding / ATP binding / identical protein binding
Similarity search - Function
Glycine-tRNA ligase, bacterial / Glycyl-tRNA synthetase / Glycyl-tRNA synthetase-like core domain / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / 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 ...Glycine-tRNA ligase, bacterial / Glycyl-tRNA synthetase / Glycyl-tRNA synthetase-like core domain / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / 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. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Glycine--tRNA ligase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.4 Å
AuthorsArnez, J.G. / Moras, D.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Glycyl-tRNA synthetase uses a negatively charged pit for specific recognition and activation of glycine.
Authors: Arnez, J.G. / Dock-Bregeon, A.C. / Moras, D.
#1: Journal: Embo J. / Year: 1995
Title: Crystal structure of glycyl-tRNA synthetase from Thermus thermophilus.
Authors: Logan, D.T. / Mazauric, M.H. / Kern, D. / Moras, D.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallisation of the glycyl-tRNA synthetase from Thermus thermophilus and initial crystallographic data.
Authors: Logan, D.T. / Cura, V. / Touzel, J.P. / Kern, D. / Moras, D.
History
DepositionJan 27, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 28, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3May 31, 2017Group: Database references / Source and taxonomy / Structure summary
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycine--tRNA ligase
B: Glycine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3044
Polymers102,2902
Non-polymers1,0142
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-17 kcal/mol
Surface area34080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)124.800, 250.900, 105.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.634886, -0.710321, 0.303914), (-0.709285, 0.379903, -0.593791), (0.306325, -0.592551, -0.745015)
Vector: 54.2396, 68.1798, 94.0248)

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Components

#1: Protein Glycine--tRNA ligase / EC 6.1.1.14 / Glycyl-tRNA synthetase / GlyRS


Mass: 51144.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ATP BOUND IN ACTIVE SITE OF EACH MONOMER
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Species: Thermus thermophilus / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: glyQS, glyS, TTHA0543 / Plasmid: PGRS / Gene (production host): GLYS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYS / References: UniProt: P56206, glycine-tRNA ligase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA P56206 96 - 158 GAP IN PDB ENTRY B P56206 96 - 158 GAP IN PDB ENTRY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 297 K / pH: 8 / Details: pH 8.0, temperature 297K
Components of the solutions
IDNameCrystal-IDSol-ID
1ETHANOLAMINE11
2MGCL211
3(NH4)2SO411
4tris-Cl11
5(NH4)2SO412
6tris-Cl12
Crystal grow
*PLUS
Temperature: 24 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.02 mMGlyRS1drop
25 mMATP1dropor 50 mM ethanolamine
32 mM1dropMgCl2
40.4 Mammonium sulfate1drop
550 mMTris-HCl1drop
60.1 MTris-HCl1reservoir
71.0-1.4 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 272 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 23, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.3→15 Å / Num. all: 20177 / Num. obs: 20177 / % possible obs: 81 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.095 / Rsym value: 9.5
Reflection
*PLUS

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
AUTOMARdata reduction
X-PLORphasing
RefinementMethod to determine structure: OTHER / Resolution: 3.4→9 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: FINAL RMS COORD. SHIFT 0.012 ANGSTROMS
RfactorNum. reflection% reflectionSelection details
Rfree0.318 713 4 %RANDOM
Rwork0.227 ---
obs-17881 83 %-
Displacement parametersBiso mean: 43.4 Å2
Refine analyzeLuzzati d res low obs: 9 Å
Refinement stepCycle: LAST / Resolution: 3.4→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7211 0 62 2 7275
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.888
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.52
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 3.4→3.55 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3878 77 4 %
Rwork0.2915 1876 -
obs--73.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM_NDBX.DNATOP_NDBX.DNA
X-RAY DIFFRACTION3PARAM.WATTOPO.WAT
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.4 Å / Lowest resolution: 9 Å / σ(F): 2 / % reflection Rfree: 4 % / Rfactor obs: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 43.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.52
LS refinement shell
*PLUS
Highest resolution: 3.4 Å / % reflection Rfree: 4 %

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