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- PDB-8t5n: Crystal Structure of Glycine--tRNA ligase from Mycobacterium tube... -

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Basic information

Entry
Database: PDB / ID: 8t5n
TitleCrystal Structure of Glycine--tRNA ligase from Mycobacterium tuberculosis (AMP-Mg bound)
ComponentsGlycine--tRNA ligase
KeywordsLIGASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Glycine--tRNA ligase
Function / homology
Function and homology information


microvesicle / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / glycyl-tRNA aminoacylation / glycine-tRNA ligase / glycine-tRNA ligase activity / diadenosine tetraphosphate biosynthetic process / tRNA aminoacylation for protein translation / extracellular vesicle / protein dimerization activity / extracellular exosome ...microvesicle / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / glycyl-tRNA aminoacylation / glycine-tRNA ligase / glycine-tRNA ligase activity / diadenosine tetraphosphate biosynthetic process / tRNA aminoacylation for protein translation / extracellular vesicle / protein dimerization activity / extracellular exosome / ATP binding / plasma membrane / cytosol / 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 / IMIDAZOLE / Glycine--tRNA ligase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 tuberculosis (AMP-Mg bound)
Authors: Seibold, S. / Lovell, S. / Battaile, K.P. / DeRocher, A.
History
DepositionJun 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,47313
Polymers54,4751
Non-polymers99812
Water6,630368
1
A: Glycine--tRNA ligase
hetero molecules

A: Glycine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,94626
Polymers108,9502
Non-polymers1,99524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area11330 Å2
ΔGint-23 kcal/mol
Surface area30470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.355, 126.355, 129.027
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-891-

HOH

21A-932-

HOH

31A-938-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 54475.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: glyQS, glyS, Rv2357c, MTCY27.23, MTCY98.26 / Plasmid: MytuD.19107.a.UW1
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: P9WFV7, glycine-tRNA ligase

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Non-polymers , 7 types, 380 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C3H5N2
#7: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.73 Å3/Da / Density % sol: 54.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus A2: 20%(v/v) Ethylene glycol, 10%(w/v) PEG 8000, 100 mM Imidazole/MES, pH 6.5, 30 mM MgCl2 and 30 mM CaCl2. MytuD.19107.a.UW1.PS38711 at 24.9 mg/mL. 10 mM MgCl2, 1 mM ATP added ...Details: Morpheus A2: 20%(v/v) Ethylene glycol, 10%(w/v) PEG 8000, 100 mM Imidazole/MES, pH 6.5, 30 mM MgCl2 and 30 mM CaCl2. MytuD.19107.a.UW1.PS38711 at 24.9 mg/mL. 10 mM MgCl2, 1 mM ATP added prior to crystallization. ATP hydrolyzed to AMP. plate 13247 well A2 drop 1. Puck: PSL-0301, Cryo: direct

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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: May 20, 2023
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: 1.65→45.14 Å / Num. obs: 73239 / % possible obs: 100 % / Redundancy: 35.1 % / CC1/2: 1 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.021 / Rrim(I) all: 0.125 / Χ2: 1 / Net I/σ(I): 19.4 / Num. measured all: 2570575
Reflection shellResolution: 1.65→1.68 Å / % possible obs: 100 % / Redundancy: 36.3 % / Rmerge(I) obs: 2.489 / Num. measured all: 128822 / Num. unique obs: 3553 / CC1/2: 0.886 / Rpim(I) all: 0.417 / Rrim(I) all: 2.524 / Χ2: 1 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4933: ???)refinement
XDSdata reduction
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→40.03 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1706 3693 5.05 %
Rwork0.1558 --
obs0.1565 73150 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→40.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3207 0 65 368 3640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093393
X-RAY DIFFRACTIONf_angle_d0.9764600
X-RAY DIFFRACTIONf_dihedral_angle_d13.7481238
X-RAY DIFFRACTIONf_chiral_restr0.059485
X-RAY DIFFRACTIONf_plane_restr0.013599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.25081430.22112640X-RAY DIFFRACTION100
1.67-1.690.20511520.21082595X-RAY DIFFRACTION100
1.69-1.720.19791260.20562647X-RAY DIFFRACTION100
1.72-1.740.2511490.22712609X-RAY DIFFRACTION100
1.74-1.770.22261250.22152661X-RAY DIFFRACTION100
1.77-1.80.2371530.20592623X-RAY DIFFRACTION100
1.8-1.830.21181370.1842626X-RAY DIFFRACTION100
1.83-1.870.1961320.1752648X-RAY DIFFRACTION100
1.87-1.90.1771350.16482657X-RAY DIFFRACTION100
1.9-1.940.17811360.15922641X-RAY DIFFRACTION100
1.94-1.980.20211500.14992633X-RAY DIFFRACTION100
1.98-2.030.16721440.14812636X-RAY DIFFRACTION100
2.03-2.080.17081230.14272668X-RAY DIFFRACTION100
2.08-2.140.15181470.14932645X-RAY DIFFRACTION100
2.14-2.20.1711450.15442641X-RAY DIFFRACTION100
2.2-2.270.16191240.14762677X-RAY DIFFRACTION100
2.27-2.350.17261540.14342654X-RAY DIFFRACTION100
2.35-2.440.17051370.13872682X-RAY DIFFRACTION100
2.44-2.560.15921290.1392676X-RAY DIFFRACTION100
2.56-2.690.14651720.14262661X-RAY DIFFRACTION100
2.69-2.860.17051400.14472677X-RAY DIFFRACTION100
2.86-3.080.16551520.1542703X-RAY DIFFRACTION100
3.08-3.390.16811520.15262703X-RAY DIFFRACTION100
3.39-3.880.15881280.14722749X-RAY DIFFRACTION100
3.88-4.880.14021630.12972773X-RAY DIFFRACTION100
4.89-40.030.20481450.19342932X-RAY DIFFRACTION99
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)
10.9176-0.49760.00531.3881-0.35540.50290.06440.1081-0.1091-0.0946-0.03340.05270.1113-0.0653-0.01890.20320.0057-0.01430.2086-0.0370.174447.493322.66412.4012
24.08190.13620.11634.73270.00962.9842-0.00220.33-0.203-0.324-0.0020.81880.2755-0.5193-0.00830.2052-0.0381-0.02630.3519-0.04530.393722.905823.12256.3267
31.0358-0.4511-0.13871.1682-0.03351.10420.07230.1685-0.0178-0.0989-0.05750.11560.0457-0.1614-0.00850.15960.0089-0.00480.218-0.01050.17137.161436.2957-3.0181
43.8737-0.4708-0.02912.38120.37592.21130.05850.11770.01890.1057-0.0386-0.52360.11520.4173-0.00490.21160.0417-0.01190.23170.00020.31172.51422.12881.842
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 70 )
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 164 )
3X-RAY DIFFRACTION3chain 'A' and (resid 165 through 342 )
4X-RAY DIFFRACTION4chain 'A' and (resid 353 through 461 )

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