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- PDB-2pmf: The crystal structure of a human glycyl-tRNA synthetase mutant -

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Basic information

Entry
Database: PDB / ID: 2pmf
TitleThe crystal structure of a human glycyl-tRNA synthetase mutant
ComponentsGlycyl-tRNA synthetase
KeywordsLIGASE / classIIa aminoacyl-tRNA synthetase
Function / homology
Function and homology information


mitochondrial glycyl-tRNA aminoacylation / ATP:ATP adenylyltransferase activity / glycine-tRNA ligase / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / glycine-tRNA ligase 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 / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / 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 / 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: 2.85 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 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9333
Polymers78,8051
Non-polymers1282
Water3,639202
1
A: Glycyl-tRNA synthetase
hetero molecules

A: Glycyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,8656
Polymers157,6102
Non-polymers2554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6120 Å2
ΔGint-59 kcal/mol
Surface area46600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.412, 91.412, 246.814
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsThe other monomer of the biological assembly is generated by the operation: y,x+1,-z

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Components

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


Mass: 78804.969 Da / Num. of mol.: 1 / Mutation: G526R
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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 3.32 Å3/Da / Density % sol: 62.9 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / 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: 2.85→50 Å / Num. obs: 25080 / % possible obs: 99.1 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.066 / Χ2: 1.021 / Net I/σ(I): 15
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 14 % / Rmerge(I) obs: 0.37 / Num. unique all: 2419 / Χ2: 1.09 / % possible all: 98.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The native T.thermophilus GlyRS structure

Resolution: 2.85→29.24 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.876 / SU B: 11.878 / SU ML: 0.238 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.559 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1272 5.1 %RANDOM
Rwork0.231 ---
obs0.233 24999 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.094 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.85→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4144 0 7 202 4353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0224242
X-RAY DIFFRACTIONr_angle_refined_deg0.8471.9485727
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7195519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.66523.762210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.96215722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9021531
X-RAY DIFFRACTIONr_chiral_restr0.0780.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023260
X-RAY DIFFRACTIONr_nbd_refined0.2290.32037
X-RAY DIFFRACTIONr_nbtor_refined0.3260.52860
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.5347
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.364
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3350.56
X-RAY DIFFRACTIONr_mcbond_it4.78332651
X-RAY DIFFRACTIONr_mcangle_it7.07444180
X-RAY DIFFRACTIONr_scbond_it3.34121764
X-RAY DIFFRACTIONr_scangle_it4.90431547
LS refinement shellResolution: 2.851→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 96 -
Rwork0.288 1614 -
obs-1710 94.53 %

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