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- PDB-1ati: CRYSTAL STRUCTURE OF GLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS -

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Basic information

Entry
Database: PDB / ID: 1ati
TitleCRYSTAL STRUCTURE OF GLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS
Components
  • (GLYCYL-tRNA SYNTHETASEGlycine—tRNA ligase) x 2
  • GLYCYL-TRNA SYNTHETASEGlycine—tRNA ligase
KeywordsPROTEIN BIOSYNTHESIS / LIGASE / SYNTHETASE / AMINOACYL-TRNA 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
Glycine--tRNA ligase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.75 Å
AuthorsLogan, D.T. / Mazauric, M.-H. / Kern, D. / Moras, D.
Citation
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.
#1: 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
DepositionApr 23, 1996Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCYL-TRNA SYNTHETASE
B: GLYCYL-TRNA SYNTHETASE
C: GLYCYL-tRNA SYNTHETASE
D: GLYCYL-tRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)120,8754
Polymers120,8754
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.900, 255.300, 105.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.613, -0.728, 0.307), (-0.729, 0.372, -0.574), (0.304, -0.576, -0.759)
Vector: 56.16, 69.07, 93.387)

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Components

#1: Protein GLYCYL-TRNA SYNTHETASE / Glycine—tRNA ligase / GLYCINE-TRNA LIGASE


Mass: 58163.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: SOME UNKNOWN RESIDUES ARE LISTED AS CHAINS C AND D. SEE REMARK 6 FOR DETAILS.
Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P56206, glycine-tRNA ligase
#2: Protein/peptide GLYCYL-tRNA SYNTHETASE / Glycine—tRNA ligase


Mass: 3166.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#3: Protein/peptide GLYCYL-tRNA SYNTHETASE / Glycine—tRNA ligase


Mass: 1379.692 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 8

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
13.5261THE TWO SYNCHROTRON DATA SETS WERE MERGED TO GIVE THE FINAL NATIVE DATA SET (TOTAL REDUNDANCY: 2.0; TOTAL MERGING R-FACTOR: 0.100).
2
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 15 ℃ / Method: vapor diffusion, hanging drop / Details: Logan, D.T., (1994) J.Mol.Biol., 241, 732.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16-8 mg/mlGlyRS1drop
25-7 %PEG60001reservoir
30.8-1.4 M1reservoirNaCl

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12771
22772
1,21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONLURE DW3210.91
SYNCHROTRONEMBL/DESY, HAMBURG X3120.927
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATENov 10, 1992
MARRESEARCH2IMAGE PLATEDec 15, 1993
Radiation
IDMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Mx-ray1
2Mx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.911
20.9271
ReflectionHighest resolution: 2.9 Å / Num. obs: 33033 / % possible obs: 90.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.01

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.75→20 Å / σ(F): 0
Details: RESIDUES 91 - 158 IN BOTH MONOMERS ARE UNCLEAR DUE TO CRYSTALLINE DISORDER. NEVERTHELESS THE AUTHORS HAVE BEEN ABLE TO BUILD SOME OF THE RESIDUES INTO THE WEAK DENSITY. THE NUMBERS GIVEN FOR ...Details: RESIDUES 91 - 158 IN BOTH MONOMERS ARE UNCLEAR DUE TO CRYSTALLINE DISORDER. NEVERTHELESS THE AUTHORS HAVE BEEN ABLE TO BUILD SOME OF THE RESIDUES INTO THE WEAK DENSITY. THE NUMBERS GIVEN FOR THE INTERVENING RESIDUES ARE ARBITRARY, SINCE THEIR IDENTITY IS NOT DISCERNIBLE FROM THE DENSITY AND THUS THEIR POSITION IN THE SEQUENCE IS NOT KNOWN. THE STRUCTURE BETWEEN 91 AND 158, WHERE PRESENT, IS BUILT AS POLY-ALA, WITH THE EXCEPTION OF 3 GLYCINES WHERE IT WAS APPARENT THAT THERE WAS NO SIDE CHAIN. THESE RESIDUES ARE PRESENTED AS CHAINS C AND D WITH RESIDUES NAMED UNK. THE MEAN OVERALL B-FACTOR IS HIGH. HOWEVER, ALMOST ALL RESIDUES IN THE CORE OF THE CATALYTIC DOMAIN HAVE B-FACTORS UNDER 50 SQUARE ANGSTROMS. THE HIGH AVERAGE IS EXACERBATED BY THE DISORDERED DOMAIN AND DISORDERED SURFACE LOOPS. THE GEOMETRY OF RESIDUES IN THE DISORDERED DOMAIN IS SLIGHTLY POORER THAN THAT IN THE CORE OF THE STRUCTURE AS IT WAS DIFFICULT TO BUILD INTO THE WEAK DENSITY. ALL THE FEW SHORT SYMMETRY CONTACTS (LESS THAN 2.2A) INVOLVE RESIDUES IN PARTLY DISORDERED LOOPS FOR WHICH THE ATOMIC POSITIONS ARE NOT WELL DEFINED. ALL THE FEW SHORT SYMMETRY CONTACTS (LESS THAN 2.2A) INVOLVE RESIDUES IN PARTLY DISORDERED LOOPS FOR WHICH THE ATOMIC POSITIONS ARE NOT WELL DEFINED.
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1832 4.8 %RANDOM
Rwork0.227 ---
obs0.227 36168 84.3 %-
Displacement parametersBiso mean: 70.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å / Luzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.45 Å
Refinement stepCycle: LAST / Resolution: 2.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7384 0 0 23 7407
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.83
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.65
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.11.5
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it3.71.5
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Rms dev Biso : 3.3 Å2 / Rms dev position: 0.2 Å / Weight Biso : 2

Ens-IDDom-IDNCS model detailsWeight position
11RESTRAINED400
2230
LS refinement shellResolution: 2.75→2.8 Å
RfactorNum. reflection% reflection
Rfree0.441 49 6.5 %
Rwork0.387 710 -
obs--33.4 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.65

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