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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 / homologyGlycyl-tRNA synthetase / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Anticodon binding domain / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding domain superfamily / Glycyl-tRNA synthetase-like core domain / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / Glycine-tRNA ligase, bacterial ...Glycyl-tRNA synthetase / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Anticodon binding domain / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding domain superfamily / Glycyl-tRNA synthetase-like core domain / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / Glycine-tRNA ligase, bacterial / Anticodon-binding / glycine-tRNA ligase complex / glycine-tRNA ligase / glycine-tRNA ligase activity / glycyl-tRNA aminoacylation / glycine binding / protein dimerization activity / magnesium ion binding / protein homodimerization activity / ATP binding / Glycine--tRNA ligase
Function and homology information
Specimen sourceThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / 3.4 Å resolution
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: New Functional Domains and Substrate Specificity
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. / Cura, V. / Touzel, J.-P. / Kern, D. / Moras, D.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 27, 1999 / Release: Jan 28, 1999
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 28, 1999Structure modelrepositoryInitial release
1.1Oct 16, 2007Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Source and taxonomy / Version format compliance
1.3May 31, 2017Structure modelDatabase references / Source and taxonomy / Structure summary
1.4Oct 4, 2017Structure modelRefinement descriptionsoftware_software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Polyers102,2902
Non-polymers1,0142
Water362
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)8270
ΔGint (kcal/M)-17
Surface area (Å2)34080
MethodPISA,PQS
Unit cell
γ
α
β
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-MC 2 2 21

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Components

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


Mass: 51144.949 Da / Num. of mol.: 2 / Details: ATP BOUND IN ACTIVE SITE OF EACH MONOMER
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Genus: Thermus / Species: Thermus thermophilus / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: glyQS, glyS, TTHA0543 / Plasmid name: PGRS / Genus (production host): Escherichia / 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


Mass: 507.181 Da / Num. of mol.: 2 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Formula: H2O / Water
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 / Density percent sol: 61 %
Crystal growTemp: 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
Temp: 24 ℃ / Method: vapor diffusion, hanging drop
Crystal grow comp
*PLUS

Crystal ID: 1

IDConcCommon nameSol IDDetailsChemical formula
10.02 mMGlyRSdrop
25 mMATPdropor 50 mM ethanolamine
32 mMdropMgCl2
40.4 Mammonium sulfatedrop
550 mMTris-HCldrop
60.1 MTris-HClreservoir
71.0-1.4 Mammonium sulfatereservoir

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Data collection

DiffractionMean temperature: 272 kelvins
SourceSource: SYNCHROTRON / Type: LURE BEAMLINE DW32 / Synchrotron site: LURE / Beamline: DW32 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Collection date: Apr 23, 1996
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionD resolution high: 3.3 Å / D resolution low: 15 Å / Number all: 20177 / Number obs: 20177 / Observed criterion sigma I: 0 / Rmerge I obs: 0.095 / Rsym value: 9.5 / Redundancy: 3.4 % / Percent possible obs: 81

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
AUTOMARdata reduction
X-PLORphasing
RefineMethod to determine structure: OTHER / Details: FINAL RMS COORD. SHIFT 0.012 ANGSTROMS / R Free selection details: RANDOM / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 2
Displacement parametersB iso mean: 43.4 Å2
Least-squares processR factor R free: 0.318 / R factor R work: 0.227 / Highest resolution: 3.4 Å / Lowest resolution: 9 Å / Number reflection R free: 713 / Number reflection obs: 17881 / Percent reflection R free: 4 / Percent reflection obs: 83
Refine analyzeLuzzati d res low obs: 9 Å
Refine hist #LASTHighest resolution: 3.4 Å / Lowest resolution: 9 Å
Number of atoms included #LASTProtein: 7211 / Nucleic acid: 0 / Ligand: 62 / Solvent: 2 / Total: 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
Refine LS shellHighest resolution: 3.4 Å / R factor R free: 0.3878 / R factor R work: 0.2915 / Lowest resolution: 3.55 Å / Number reflection R free: 77 / Number reflection R work: 1876 / Total number of bins used: 8 / Percent reflection R free: 4 / Percent reflection 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
Refine
*PLUS
Sigma F: 2
Displacement parameters
*PLUS
B iso mean: 43.4 Å2
Least-squares process
*PLUS
R factor obs: 0.227 / Highest resolution: 3.4 Å / Lowest resolution: 9 Å / Percent reflection R free: 4
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.90
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.52
Refine LS shell
*PLUS
Highest resolution: 3.4 Å / Percent reflection R free: 4

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