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- PDB-5f5w: Crystal structure of the alpha subunit of glycyl tRNA synthetase ... -

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Basic information

Entry
Database: PDB / ID: 5f5w
TitleCrystal structure of the alpha subunit of glycyl tRNA synthetase (GlyRS) from Aquifex aeolicus in complex with an analog of glycyl adenylate (Gly-SA)
ComponentsGlycine--tRNA ligase alpha subunit
KeywordsLIGASE / class II tRNA synthetase
Function / homology
Function and homology information


glycyl-tRNA aminoacylation / glycine-tRNA ligase / glycine-tRNA ligase activity / ATP binding / cytoplasm
Similarity search - Function
Class II aaRS and biotin synthetases; domain 2 / Glycine-tRNA ligase, alpha subunit / Glycine-tRNA synthetase, heterodimeric / Glycyl-tRNA synthetase alpha subunit / Heterodimeric glycyl-transfer RNA synthetases family profile. / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle ...Class II aaRS and biotin synthetases; domain 2 / Glycine-tRNA ligase, alpha subunit / Glycine-tRNA synthetase, heterodimeric / Glycyl-tRNA synthetase alpha subunit / Heterodimeric glycyl-transfer RNA synthetases family profile. / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5'-O-(glycylsulfamoyl)adenosine / Glycine--tRNA ligase alpha subunit
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsValencia-Sanchez, M.I. / Torres-Larios, A.
Funding support Mexico, 2items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)PDCPN2014-247543 Mexico
UNAM-PAPIITIN202416 Mexico
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Insights into the Polyphyletic Origins of Glycyl tRNA Synthetases.
Authors: Valencia-Sanchez, M.I. / Rodriguez-Hernandez, A. / Ferreira, R. / Santamaria-Suarez, H.A. / Arciniega, M. / Dock-Bregeon, A.C. / Moras, D. / Beinsteiner, B. / Mertens, H. / Svergun, D. / ...Authors: Valencia-Sanchez, M.I. / Rodriguez-Hernandez, A. / Ferreira, R. / Santamaria-Suarez, H.A. / Arciniega, M. / Dock-Bregeon, A.C. / Moras, D. / Beinsteiner, B. / Mertens, H. / Svergun, D. / Brieba, L.G. / Grtli, M. / Torres-Larios, A.
History
DepositionDec 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Jul 20, 2016Group: Data collection
Revision 1.3Jul 27, 2016Group: Database references
Revision 1.4Jan 15, 2020Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycine--tRNA ligase alpha subunit
B: Glycine--tRNA ligase alpha subunit
C: Glycine--tRNA ligase alpha subunit
D: Glycine--tRNA ligase alpha subunit
E: Glycine--tRNA ligase alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,75810
Polymers177,7415
Non-polymers2,0175
Water362
1
A: Glycine--tRNA ligase alpha subunit
hetero molecules

A: Glycine--tRNA ligase alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9034
Polymers71,0962
Non-polymers8072
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area4990 Å2
ΔGint-31 kcal/mol
Surface area21550 Å2
MethodPISA
2
B: Glycine--tRNA ligase alpha subunit
C: Glycine--tRNA ligase alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9034
Polymers71,0962
Non-polymers8072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-33 kcal/mol
Surface area21260 Å2
MethodPISA
3
D: Glycine--tRNA ligase alpha subunit
E: Glycine--tRNA ligase alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9034
Polymers71,0962
Non-polymers8072
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-31 kcal/mol
Surface area20870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.829, 130.010, 145.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 35548.191 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: glyQ, aq_945 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O67081, glycine-tRNA ligase
#2: Chemical
ChemComp-G5A / 5'-O-(glycylsulfamoyl)adenosine


Mass: 403.371 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H17N7O7S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: 2.72 Å3/Da / Density % sol: 57 % / Description: needles
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: Drops containing 1 microliter of alpha-AaGlyRS at 15 mg/ml yielded crystals at 18C when mixed with 1 microliter of a reservoir solution containing 30% polyethylene glycol monomethyl ether ...Details: Drops containing 1 microliter of alpha-AaGlyRS at 15 mg/ml yielded crystals at 18C when mixed with 1 microliter of a reservoir solution containing 30% polyethylene glycol monomethyl ether 2000 and 100 mM potassium thiocyanate. Crystals were soaked for 2 days in a solution containing a final concentration of 28 mM GSAd by mixing 1.3 microliters of the drop containing crystals, 2.5 microliters of reservoir solution and 1.5 microliters of GSAd at 100 mM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.81→83.43 Å / Num. all: 47824 / Num. obs: 47824 / % possible obs: 100 % / Redundancy: 4.4 % / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 9.7
Reflection shellResolution: 2.81→2.91 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
Aimless0.5.10data scaling
MOSFLM7.2.1data reduction
BALBES1.1.5phasing
Coot0.8.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J5W

1j5w


Resolution: 2.81→80.166 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2521 2409 5.05 %random selection
Rwork0.2389 ---
obs0.2396 47741 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.81→80.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11740 0 135 2 11877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112218
X-RAY DIFFRACTIONf_angle_d1.46216572
X-RAY DIFFRACTIONf_dihedral_angle_d16.3364511
X-RAY DIFFRACTIONf_chiral_restr0.0981676
X-RAY DIFFRACTIONf_plane_restr0.0072122
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.86740.3631510.36282607X-RAY DIFFRACTION100
2.8674-2.92970.38761470.3442614X-RAY DIFFRACTION100
2.9297-2.99790.36421270.33722657X-RAY DIFFRACTION100
2.9979-3.07290.34251590.3112619X-RAY DIFFRACTION100
3.0729-3.15590.31981160.3032644X-RAY DIFFRACTION100
3.1559-3.24880.3541440.28312656X-RAY DIFFRACTION100
3.2488-3.35370.30991090.28522657X-RAY DIFFRACTION100
3.3537-3.47350.25411530.27622617X-RAY DIFFRACTION100
3.4735-3.61260.27341530.25172661X-RAY DIFFRACTION100
3.6126-3.7770.26241290.24122655X-RAY DIFFRACTION100
3.777-3.97620.24211350.22762651X-RAY DIFFRACTION100
3.9762-4.22530.22761380.22882683X-RAY DIFFRACTION100
4.2253-4.55150.24841390.21442684X-RAY DIFFRACTION100
4.5515-5.00940.21291570.20212668X-RAY DIFFRACTION100
5.0094-5.73420.19111400.21322709X-RAY DIFFRACTION100
5.7342-7.22370.23281470.21882731X-RAY DIFFRACTION100
7.2237-80.19890.2061650.18862819X-RAY DIFFRACTION99

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