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- PDB-8sld: Crystal Structure of Glycine tRNA ligase from Mycobacterium therm... -

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Basic information

Entry
Database: PDB / ID: 8sld
TitleCrystal Structure of Glycine tRNA ligase from Mycobacterium thermoresistibile (Apo)
ComponentsGlycine--tRNA ligase
KeywordsLIGASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homology
Function and homology information


glycyl-tRNA aminoacylation / glycine-tRNA ligase / glycine-tRNA ligase activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Glycine-tRNA ligase, bacterial / Glycyl-tRNA synthetase / Glycyl-tRNA synthetase-like core domain / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / 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 / Aminoacyl-tRNA synthetase, class II ...Glycine-tRNA ligase, bacterial / Glycyl-tRNA synthetase / Glycyl-tRNA synthetase-like core domain / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / 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 / 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)
Similarity search - Domain/homology
Glycine--tRNA ligase
Similarity search - Component
Biological speciesMycolicibacterium thermoresistibile ATCC 19527 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of Glycine tRNA ligase from Mycobacterium thermoresistibile (Apo)
Authors: Lovell, S. / Liu, L. / Battaile, K.P. / Seibold, S.
History
DepositionApr 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1052
Polymers55,0811
Non-polymers241
Water00
1
A: Glycine--tRNA ligase
hetero molecules

A: Glycine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,2104
Polymers110,1612
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation27_555-x+1/2,y,-z1
Buried area3720 Å2
ΔGint-20 kcal/mol
Surface area29440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.848, 190.848, 190.848
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132

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Components

#1: Protein Glycine--tRNA ligase


Mass: 55080.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium thermoresistibile ATCC 19527 (bacteria)
Gene: glyQS / Plasmid: MythA.19107.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G7CIG9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN

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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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: JCSG+ H8: 25% (w/v) PEG 3350, 0.2M NaCl, 0.1M Bis-Tris pH 5.5, MythA.19107.a.A1.PW39162 at 17 mg/mL. Plate: Clover 1/12/2023 AMP, F10. Puck: PSL-1504, Cryo: 25% PEG200 + 85% crystallant. 2mM ...Details: JCSG+ H8: 25% (w/v) PEG 3350, 0.2M NaCl, 0.1M Bis-Tris pH 5.5, MythA.19107.a.A1.PW39162 at 17 mg/mL. Plate: Clover 1/12/2023 AMP, F10. Puck: PSL-1504, Cryo: 25% PEG200 + 85% crystallant. 2mM AMP added prior to crystallization but not observed in the structure

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 14, 2022
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.85→47.71 Å / Num. obs: 14177 / % possible obs: 100 % / Redundancy: 80.2 % / CC1/2: 1 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.02 / Rrim(I) all: 0.177 / Χ2: 1 / Net I/σ(I): 30.8 / Num. measured all: 1137228
Reflection shellResolution: 2.85→3 Å / % possible obs: 100 % / Redundancy: 85.2 % / Rmerge(I) obs: 3.704 / Num. measured all: 172041 / Num. unique obs: 2020 / CC1/2: 0.784 / Rpim(I) all: 0.402 / Rrim(I) all: 3.726 / Χ2: 0.97 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→44.98 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2652 679 4.8 %
Rwork0.233 --
obs0.2344 14147 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→44.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2702 0 1 0 2703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022763
X-RAY DIFFRACTIONf_angle_d0.4353747
X-RAY DIFFRACTIONf_dihedral_angle_d11.9141014
X-RAY DIFFRACTIONf_chiral_restr0.041405
X-RAY DIFFRACTIONf_plane_restr0.004486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.070.38291310.32962628X-RAY DIFFRACTION100
3.07-3.380.32511590.30262617X-RAY DIFFRACTION100
3.38-3.870.30551270.27782673X-RAY DIFFRACTION100
3.87-4.870.24281390.20672700X-RAY DIFFRACTION100
4.87-44.980.23641230.20852850X-RAY DIFFRACTION100
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)
16.68971.5593.06471.96020.89159.0697-0.07080.13390.2947-0.04680.0609-0.0523-0.42810.19550.05850.47160.0496-0.06550.40950.09440.527646.8771-23.168314.0364
25.28540.0378-1.74212.6118-1.19385.62920.29830.42120.0235-0.02040.31840.5318-0.1518-0.5464-0.65710.6170.0004-0.03210.6620.21080.727929.39-21.0018-0.6691
32.9476-0.85431.42592.3691-2.81816.67680.3631-0.12460.1122-0.34790.42070.4351-0.0877-0.9667-0.71640.6899-0.04760.08090.6920.15880.718728.057-17.97562.6351
45.62871.5189-1.44326.1862-0.65246.34810.1867-0.82540.0580.53330.43490.6652-0.16750.1236-0.43390.6060.0072-0.08160.65010.07780.756745.3766-34.940921.548
54.5182-0.48912.9856.1930.16693.36990.1558-0.8006-1.35430.4410.1229-0.49370.58320.2328-0.21120.84320.1518-0.19130.88110.17991.069257.0253-44.421816.8226
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 264 )
3X-RAY DIFFRACTION3chain 'A' and (resid 265 through 342 )
4X-RAY DIFFRACTION4chain 'A' and (resid 343 through 367 )
5X-RAY DIFFRACTION5chain 'A' and (resid 368 through 460 )

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