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- PDB-2pme: The Apo crystal Structure of the glycyl-tRNA synthetase -

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Basic information

Entry
Database: PDB / ID: 2pme
TitleThe Apo crystal Structure of the glycyl-tRNA synthetase
ComponentsGlycyl-tRNA synthetase
KeywordsLIGASE / ClassIIa aminoacyl tRNA synthetase
Function / homology
Function and homology information


mitochondrial glycyl-tRNA aminoacylation / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / glycine-tRNA ligase / glycine-tRNA ligase activity / Mitochondrial tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / secretory granule / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases ...mitochondrial glycyl-tRNA aminoacylation / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / glycine-tRNA ligase / glycine-tRNA ligase activity / Mitochondrial tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / secretory granule / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / protein dimerization activity / mitochondrial matrix / axon / mitochondrion / extracellular exosome / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Herpes Virus-1 - #230 / Glycyl-tRNA synthetase / Glycyl-tRNA synthetase-like core domain / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Anticodon-binding domain ...Herpes Virus-1 - #230 / Glycyl-tRNA synthetase / Glycyl-tRNA synthetase-like core domain / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Anticodon-binding domain / 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 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Herpes Virus-1 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / S15/NS1, RNA-binding / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glycine--tRNA ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsXie, W.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Long-range structural effects of a Charcot-Marie- Tooth disease-causing mutation in human glycyl-tRNA synthetase.
Authors: Xie, W. / Nangle, L.A. / Zhang, W. / Schimmel, P. / Yang, X.L.
History
DepositionApr 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)78,7051
Polymers78,7051
Non-polymers00
Water2,198122
1
A: Glycyl-tRNA synthetase

A: Glycyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)157,4102
Polymers157,4102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5310 Å2
ΔGint-38 kcal/mol
Surface area47420 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.742, 91.742, 247.176
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is a dimer generated asymmetric unit by the operations: y,x,-z

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Components

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


Mass: 78704.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GARS / Plasmid: pET21a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P41250, glycine-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 3.35 Å3/Da / Density % sol: 63.27 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 18765 / % possible obs: 77.1 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.099 / Χ2: 0.991 / Net I/σ(I): 9.1
Reflection shellResolution: 2.9→3 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.524 / Num. unique all: 1906 / Χ2: 0.916 / % possible all: 80.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→36.83 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.867 / SU B: 13.151 / SU ML: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.782 / ESU R Free: 0.427 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.271 978 5.2 %RANDOM
Rwork0.23 ---
obs0.232 18744 77.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.392 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.9→36.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4136 0 0 122 4258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0224229
X-RAY DIFFRACTIONr_angle_refined_deg0.7561.9495711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6325517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.30723.72207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.03915720
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6461530
X-RAY DIFFRACTIONr_chiral_restr0.0620.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.023243
X-RAY DIFFRACTIONr_nbd_refined0.2330.31978
X-RAY DIFFRACTIONr_nbtor_refined0.3250.52887
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2430.5279
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.371
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3150.56
X-RAY DIFFRACTIONr_mcbond_it4.60732644
X-RAY DIFFRACTIONr_mcangle_it6.52844170
X-RAY DIFFRACTIONr_scbond_it3.29621760
X-RAY DIFFRACTIONr_scangle_it4.83931541
LS refinement shellResolution: 2.902→2.977 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 65 -
Rwork0.308 1348 -
obs-1413 80.42 %

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