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- PDB-2zxf: Crystal structure of human glycyl-trna synthetase (GLYRS) in comp... -

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Basic information

Entry
Database: PDB / ID: 2zxf
TitleCrystal structure of human glycyl-trna synthetase (GLYRS) in complex with AP4A (cocrystallized with AP4A)
ComponentsGlycyl-tRNA synthetase
KeywordsLIGASE / AP4A / glycine / ATP / GLY-AMP / tRNA / aminoacyl-tRNA synthetase / ATP-binding / charcot-marie-tooth disease / disease mutation / nucleotide-binding / phosphoprotein / protein biosynthesis
Function / homology
Function and homology information


mitochondrial glycyl-tRNA aminoacylation / ATP:ATP adenylyltransferase activity / glycine-tRNA ligase / glycine-tRNA ligase activity / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / Mitochondrial tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / secretory granule ...mitochondrial glycyl-tRNA aminoacylation / ATP:ATP adenylyltransferase activity / glycine-tRNA ligase / glycine-tRNA ligase activity / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / Mitochondrial tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / secretory granule / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 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 / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / Anticodon-binding domain ...Herpes Virus-1 - #230 / Glycyl-tRNA synthetase / Glycyl-tRNA synthetase-like core domain / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / 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
BIS(ADENOSINE)-5'-TETRAPHOSPHATE / Glycine--tRNA ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsGuo, R.T. / Yang, X.L. / Schimmel, P.
CitationJournal: To be Published
Title: Crystal structures and biochemical analyses suggest unique mechanism and role for human GlyRS in Ap4A homeostasis
Authors: Guo, R.T. / Chong, Y.E. / Guo, M. / Yang, X.L.
History
DepositionDec 23, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Glycyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5412
Polymers78,7051
Non-polymers8361
Water1,27971
1
A: Glycyl-tRNA synthetase
hetero molecules

A: Glycyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,0824
Polymers157,4102
Non-polymers1,6732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area7690 Å2
ΔGint-43 kcal/mol
Surface area44420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.299, 137.030, 132.751
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 78704.828 Da / Num. of mol.: 1 / Fragment: UNP residues 55-739
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GARS / Plasmid: pET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P41250, glycine-tRNA ligase
#2: Chemical ChemComp-B4P / BIS(ADENOSINE)-5'-TETRAPHOSPHATE


Mass: 836.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28N10O19P4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 3.5 Å3/Da / Density % sol: 64.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25mM Tris-HCL, 150mM NaCl, 10mM MgCl2, 4M Sodium formate, PH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 20, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. all: 15555 / Num. obs: 14819 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 37.8
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 4 / Num. unique all: 1536 / % possible all: 71.5

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
XTALVIEWrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PME

2pme


Resolution: 3.4→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 682 -RANDOM
Rwork0.244 ---
all-15555 --
obs-13439 86.4 %-
Displacement parametersBiso mean: 174.9 Å2
Refine analyzeLuzzati sigma a obs: 1.3 Å
Refinement stepCycle: LAST / Resolution: 3.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4228 0 53 77 4358
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5
LS refinement shellResolution: 3.4→3.52 Å
RfactorNum. reflection% reflection
Rfree0.542 39 -
Rwork0.484 --
obs-832 54.2 %

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