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- PDB-8u2p: Crystal Structure of Glycine--tRNA ligase from Mycobacterium tube... -

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Basic information

Entry
Database: PDB / ID: 8u2p
TitleCrystal Structure of Glycine--tRNA ligase from Mycobacterium 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


microvesicle / glycyl-tRNA aminoacylation / glycine-tRNA ligase / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / glycine-tRNA ligase activity / diadenosine tetraphosphate biosynthetic process / tRNA aminoacylation for protein translation / extracellular vesicle / protein dimerization activity / extracellular exosome ...microvesicle / glycyl-tRNA aminoacylation / glycine-tRNA ligase / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / 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
5'-O-(glycylsulfamoyl)adenosine / IMIDAZOLE / Glycine--tRNA ligase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 from Mycobacterium 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
Revision 1.1Apr 10, 2024Group: Source and taxonomy / Category: 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)55,49311
Polymers54,4751
Non-polymers1,01810
Water2,306128
1
A: Glycine--tRNA ligase
hetero molecules

A: Glycine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,98722
Polymers108,9502
Non-polymers2,03620
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area9650 Å2
ΔGint-42 kcal/mol
Surface area30320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.293, 124.293, 131.383
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-688-

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, 138 molecules

#2: Chemical ChemComp-G5A / 5'-O-(glycylsulfamoyl)adenosine


Mass: 403.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17N7O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
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. Crystals grown in a clover Jr. ...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. Crystals grown in a clover Jr. plate using conditions for PDB entry 8T5N. 4 hour soak in 5mM G5A in crystallant. Plate SS-Clover book 3, pg35. Puck: PSL-1308, 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: Aug 6, 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: 2.25→49.8 Å / Num. obs: 29045 / % possible obs: 100 % / Redundancy: 30.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.036 / Rrim(I) all: 0.201 / Χ2: 1.01 / Net I/σ(I): 18.1 / Num. measured all: 890444
Reflection shellResolution: 2.25→2.32 Å / % possible obs: 100 % / Redundancy: 30.4 % / Rmerge(I) obs: 2.394 / Num. measured all: 79397 / Num. unique obs: 2616 / CC1/2: 0.718 / Rpim(I) all: 0.439 / Rrim(I) all: 2.434 / Χ2: 1 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5057: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→45.15 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2078 1464 5.05 %
Rwork0.1786 --
obs0.18 28975 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→45.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3213 0 64 128 3405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033355
X-RAY DIFFRACTIONf_angle_d0.5934549
X-RAY DIFFRACTIONf_dihedral_angle_d14.5741208
X-RAY DIFFRACTIONf_chiral_restr0.042483
X-RAY DIFFRACTIONf_plane_restr0.006588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.330.29111420.22712684X-RAY DIFFRACTION100
2.33-2.420.26651390.20912716X-RAY DIFFRACTION100
2.42-2.530.24011370.20012712X-RAY DIFFRACTION100
2.53-2.670.22021480.18142689X-RAY DIFFRACTION100
2.67-2.830.23351440.17922731X-RAY DIFFRACTION100
2.83-3.050.2111470.19082717X-RAY DIFFRACTION100
3.05-3.360.25361610.18222738X-RAY DIFFRACTION100
3.36-3.850.20311370.1742773X-RAY DIFFRACTION100
3.85-4.850.14381520.14582801X-RAY DIFFRACTION100
4.85-45.150.2161570.19082950X-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)
11.1796-0.76450.02561.4166-0.94941.05140.05150.078-0.1081-0.2671-0.0347-0.01880.2773-0.0509-0.01820.40350.0104-0.01640.3349-0.02640.308747.161122.49712.6011
22.5149-0.50890.92893.8045-0.66331.72870.02010.1469-0.3626-0.43740.18240.79040.3165-0.3213-0.24950.3952-0.0349-0.05090.55770.03580.579821.430921.77935.2517
31.3584-0.5472-0.40341.8594-0.42631.72710.07110.1211-0.009-0.2275-0.0130.13310.1282-0.235-0.05690.3369-0.0054-0.02590.39150.00890.316535.176336.2268-1.5855
41.8264-1.3534-0.29062.0965-0.24110.97230.1510.1216-0.0467-0.2522-0.2692-0.38140.20280.18730.09240.47460.05210.05960.34440.05750.440261.530522.82440.2695
52.3627-0.0853-0.06182.2822-0.53831.5401-0.00580.13550.2337-0.1691-0.2632-0.78730.12930.45550.25080.46750.06940.10140.48940.1390.693373.331122.76961.5378
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 156 )
3X-RAY DIFFRACTION3chain 'A' and (resid 157 through 318 )
4X-RAY DIFFRACTION4chain 'A' and (resid 319 through 392 )
5X-RAY DIFFRACTION5chain 'A' and (resid 393 through 461 )

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