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

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Basic information

Entry
Database: PDB / ID: 8slh
TitleCrystal Structure of Glycine tRNA ligase from Mycobacterium thermoresistibile (AMP bound, hexagonal form)
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
ADENOSINE MONOPHOSPHATE / Glycine--tRNA ligase
Similarity search - Component
Biological speciesMycolicibacterium thermoresistibile ATCC 19527 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle 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 (AMP bound, hexagonal form)
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)55,4523
Polymers55,0811
Non-polymers3722
Water00
1
A: Glycine--tRNA ligase
hetero molecules

A: Glycine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,9046
Polymers110,1612
Non-polymers7434
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area6190 Å2
ΔGint-31 kcal/mol
Surface area30150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.254, 126.254, 127.896
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


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

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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: 2.67 Å3/Da / Density % sol: 53.95 %
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, H10. Puck: PSL-1508, Cryo: 15% 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, H10. Puck: PSL-1508, Cryo: 15% PEG200 + 85% crystallant. 2mM AMP added prior to crystallization.
PH range: '

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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: 3.05→44.92 Å / Num. obs: 12003 / % possible obs: 99.9 % / Redundancy: 19.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.028 / Rrim(I) all: 0.124 / Χ2: 1.01 / Net I/σ(I): 20.5 / Num. measured all: 235374
Reflection shellResolution: 3.05→3.26 Å / % possible obs: 100 % / Redundancy: 20.9 % / Rmerge(I) obs: 1.789 / Num. measured all: 44155 / Num. unique obs: 2114 / CC1/2: 0.883 / Rpim(I) all: 0.399 / Rrim(I) all: 1.833 / Χ2: 1 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4932: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→41.55 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.15 / Phase error: 33.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2879 592 4.96 %
Rwork0.23 --
obs0.2329 11941 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.05→41.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2933 0 24 0 2957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023027
X-RAY DIFFRACTIONf_angle_d0.5254110
X-RAY DIFFRACTIONf_dihedral_angle_d11.4121106
X-RAY DIFFRACTIONf_chiral_restr0.041443
X-RAY DIFFRACTIONf_plane_restr0.005529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.360.35221460.31042754X-RAY DIFFRACTION100
3.36-3.840.31151440.26212787X-RAY DIFFRACTION100
3.84-4.840.27451330.20832836X-RAY DIFFRACTION100
4.84-41.550.27661690.22022972X-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)
13.183-2.4751-0.59985.41090.15543.77770.06360.103-0.20120.04680.13280.62310.3062-0.675-0.14530.7021-0.0379-0.06670.86660.00580.523440.350331.36760.0298
24.2064-2.5175-0.70224.4421-0.88863.19860.25190.21770.104-0.1290.01350.3680.4707-0.7041-0.22720.7936-0.0217-0.08641.05020.02240.558235.78736.9724-3.2365
34.5726-0.34860.26125.0808-0.37223.43570.19040.3437-0.16180.0001-0.549-0.75850.68770.80950.29391.04540.21480.131.09430.1010.816972.423921.95811.2643
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 264 )
2X-RAY DIFFRACTION2chain 'A' and (resid 265 through 341 )
3X-RAY DIFFRACTION3chain 'A' and (resid 342 through 459 )

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