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- PDB-8u2q: Crystal Structure of Glycine--tRNA ligase active site chimera fro... -

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Basic information

Entry
Database: PDB / ID: 8u2q
TitleCrystal Structure of Glycine--tRNA ligase active site chimera from Mycobacterium thermoresistibile/tuberculosis (G5A bound)
ComponentsGlycine--tRNA ligase
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Glycine--tRNA ligase
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
5'-O-(glycylsulfamoyl)adenosine / Glycine--tRNA ligase
Similarity search - Component
Biological speciesMycolicibacterium thermoresistibile ATCC 19527 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of Glycine--tRNA ligase active site chimera from Mycobacterium thermoresistibile/tuberculosis (G5A bound)
Authors: Seibold, S. / Lovell, S. / Battaile, K.P. / DeRocher, A.
History
DepositionSep 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycine--tRNA ligase
B: Glycine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,37710
Polymers109,3262
Non-polymers1,0518
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-61 kcal/mol
Surface area31860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.286, 87.388, 99.152
Angle α, β, γ (deg.)90.00, 104.12, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glycine--tRNA ligase


Mass: 54663.113 Da / Num. of mol.: 2 / Fragment: V122, P123 deletion / Mutation: H97Y, Q99A, D121G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium thermoresistibile ATCC 19527 (bacteria)
Gene: glyQS / Plasmid: MythA.19107.a.UX11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G7CIG9

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Non-polymers , 6 types, 115 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-G5A / 5'-O-(glycylsulfamoyl)adenosine


Mass: 403.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17N7O7S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 3.29 Å3/Da / Density % sol: 62.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Index F12: 25% (w/v) Polyethylene glycol 3,350, 0.1 M HEPES pH 7.5, 0.2 M Sodium chloride. MythA.19107.a.UX11.PW39208 at 20.4 mg/mL. 2mM G5A added prior to crystallization. Plate 13386 F12 ...Details: Index F12: 25% (w/v) Polyethylene glycol 3,350, 0.1 M HEPES pH 7.5, 0.2 M Sodium chloride. MythA.19107.a.UX11.PW39208 at 20.4 mg/mL. 2mM G5A added prior to crystallization. Plate 13386 F12 drop 3. Puck: PSL-1203, Cryo: 20% Glycerol + 80% Crystallant.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9785 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Aug 6, 2023
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.45→48.08 Å / Num. obs: 52055 / % possible obs: 99.6 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.053 / Rrim(I) all: 0.101 / Χ2: 0.94 / Net I/σ(I): 9.8 / Num. measured all: 182866
Reflection shellResolution: 2.45→2.53 Å / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.887 / Num. measured all: 16592 / Num. unique obs: 4494 / CC1/2: 0.756 / Rpim(I) all: 0.533 / Rrim(I) all: 1.037 / Χ2: 0.98 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5057: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→41.53 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2092 2606 5.02 %
Rwork0.1852 --
obs0.1864 51956 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→41.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6659 0 63 107 6829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036887
X-RAY DIFFRACTIONf_angle_d0.5729367
X-RAY DIFFRACTIONf_dihedral_angle_d14.1262481
X-RAY DIFFRACTIONf_chiral_restr0.043999
X-RAY DIFFRACTIONf_plane_restr0.0061222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.490.32431490.28342584X-RAY DIFFRACTION100
2.49-2.540.28361560.26552562X-RAY DIFFRACTION99
2.54-2.590.29991300.27392596X-RAY DIFFRACTION100
2.59-2.650.29181280.27442582X-RAY DIFFRACTION99
2.65-2.710.31441360.25682585X-RAY DIFFRACTION100
2.71-2.780.27361470.23892574X-RAY DIFFRACTION100
2.78-2.860.23011350.23072583X-RAY DIFFRACTION100
2.86-2.940.30361550.21082603X-RAY DIFFRACTION100
2.94-3.030.23161570.20522549X-RAY DIFFRACTION100
3.03-3.140.23671400.22182619X-RAY DIFFRACTION100
3.14-3.270.24491300.1982609X-RAY DIFFRACTION100
3.27-3.420.19981260.19592623X-RAY DIFFRACTION100
3.42-3.60.23871240.19262615X-RAY DIFFRACTION100
3.6-3.820.21641220.182624X-RAY DIFFRACTION99
3.82-4.120.16341310.15442581X-RAY DIFFRACTION98
4.12-4.530.14211110.13912584X-RAY DIFFRACTION98
4.53-5.190.15841370.13782596X-RAY DIFFRACTION99
5.19-6.530.19961500.17742631X-RAY DIFFRACTION99
6.53-41.530.191420.17562650X-RAY DIFFRACTION98
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)
11.95390.13110.66170.9216-0.15142.47810.04050.0994-0.2518-0.20420.12220.16010.4515-0.2306-0.1510.4963-0.116-0.00050.38420.0030.3998-24.613235.51612.2099
22.2577-0.62981.24320.8656-0.29632.55340.0290.4105-0.0298-0.2437-0.02930.07480.17630.1768-0.00540.5129-0.11860.01690.4103-0.01340.3662-21.140.7835-0.2714
32.39680.45821.19912.4804-0.03194.1175-0.0642-0.0010.1480.06920.0419-0.0659-0.05560.26720.03520.3456-0.04510.04130.4845-0.00640.4447-2.379947.587732.6692
40.43340.21910.11481.8262-0.22882.1512-0.06090.01820.0114-0.14260.01850.19170.0877-0.34560.01190.3617-0.0477-0.00580.45640.040.4163-33.419450.255316.7601
53.2510.64360.49850.87750.2712.19730.1443-0.3094-0.1058-0.12-0.24890.0751-0.2022-0.50480.11390.6709-0.1998-0.01090.72840.03450.5497-49.583330.544319.1676
60.9902-0.32930.39391.5893-0.78292.70720.0131-0.2869-0.08120.10860.08420.23360.1647-0.671-0.12360.3836-0.10070.03240.64630.03940.4481-35.10843.373732.7782
71.83480.8821-0.55641.3392-0.52152.1591-0.42110.14860.65220.05280.0438-0.1775-0.7063-0.72490.31160.6590.0726-0.15510.4255-0.0030.6337-30.216272.665812.2381
82.01020.24740.1451.95590.61092.051-0.16040.17960.3731-0.15120.1736-0.158-0.34640.02360.00920.7476-0.0537-0.09940.46180.0230.6976-19.821272.522110.6073
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 153 )
2X-RAY DIFFRACTION2chain 'A' and (resid 154 through 342 )
3X-RAY DIFFRACTION3chain 'A' and (resid 343 through 461 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 70 )
5X-RAY DIFFRACTION5chain 'B' and (resid 71 through 164 )
6X-RAY DIFFRACTION6chain 'B' and (resid 165 through 342 )
7X-RAY DIFFRACTION7chain 'B' and (resid 343 through 376 )
8X-RAY DIFFRACTION8chain 'B' and (resid 377 through 461 )

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