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- PDB-4ye6: The crystal structure of the intact human GlnRS -

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Basic information

Entry
Database: PDB / ID: 4ye6
TitleThe crystal structure of the intact human GlnRS
ComponentsGlutamine--tRNA ligase
KeywordsLIGASE / aminoacyl-tRNA synthetase / class I aaRS / L-glutamine
Function / homology
Function and homology information


glutamine-tRNA ligase / glutamine-tRNA ligase activity / glutaminyl-tRNA aminoacylation / Mitochondrial tRNA aminoacylation / Selenoamino acid metabolism / aminoacyl-tRNA synthetase multienzyme complex / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / negative regulation of stress-activated MAPK cascade / protein kinase inhibitor activity ...glutamine-tRNA ligase / glutamine-tRNA ligase activity / glutaminyl-tRNA aminoacylation / Mitochondrial tRNA aminoacylation / Selenoamino acid metabolism / aminoacyl-tRNA synthetase multienzyme complex / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / negative regulation of stress-activated MAPK cascade / protein kinase inhibitor activity / negative regulation of apoptotic signaling pathway / Transcriptional and post-translational regulation of MITF-M expression and activity / negative regulation of protein kinase activity / brain development / mitochondrial matrix / negative regulation of DNA-templated transcription / protein kinase binding / protein-containing complex / ATP binding / cytosol / cytoplasm
Similarity search - Function
Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain 2 / Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal / Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal, subdomain 1 / Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal, subdomain 2 / Glutaminyl-tRNA synthetase, non-specific RNA binding region part 2 / Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1 / Glutamine-tRNA synthetase / : / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / : ...Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain 2 / Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal / Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal, subdomain 1 / Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal, subdomain 2 / Glutaminyl-tRNA synthetase, non-specific RNA binding region part 2 / Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1 / Glutamine-tRNA synthetase / : / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / : / tRNA synthetases class I (E and Q), anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily
Similarity search - Domain/homology
Glutamine--tRNA ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsOgnjenovic, J. / Wu, J. / Ling, J. / Simonovic, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: The crystal structure of human GlnRS provides basis for the development of neurological disorders.
Authors: Ognjenovic, J. / Wu, J. / Matthies, D. / Baxa, U. / Subramaniam, S. / Ling, J. / Simonovic, M.
History
DepositionFeb 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2May 4, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.name / _software.version
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Glutamine--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)88,0591
Polymers88,0591
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)333.679, 57.983, 86.123
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Glutamine--tRNA ligase / Glutaminyl-tRNA synthetase / GlnRS


Mass: 88058.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: QARS / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: P47897, glutamine-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 4.73 Å3/Da / Density % sol: 74 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M calcium acetate, 0.1M Tris, pH 6.0, 12.5% (w/v) PEG 3,350, 60mM gly-gly-gly
PH range: 6

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionRedundancy: 1.9 % / Number: 74437 / Rmerge(I) obs: 0.332 / Χ2: 0.48 / D res high: 2.7 Å / D res low: 50 Å / Num. obs: 38336 / % possible obs: 81.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
9.225010.5161.4032.3
7.329.2210.4731.2572.5
6.47.3210.6391.8252.4
5.816.410.5151.1062.4
5.45.8110.4751.0462.4
5.085.410.3370.7182.3
4.835.0810.2290.4822.3
4.624.8310.1680.3622.2
4.444.6210.1060.2572.2
4.294.4410.0660.1362.2
4.154.2910.0830.1972.1
4.034.1510.0750.1372.1
3.934.0310.0640.1462
3.833.9310.0670.1442.1
3.743.8310.0670.1312.1
3.663.7410.0660.1592
3.593.6610.0720.142
3.523.5910.0780.1532
3.463.5210.0980.172
3.43.4610.0920.1492
3.353.410.1070.1382
3.33.3510.1070.1391.9
3.253.310.1350.1521.9
3.23.2510.1420.1531.8
3.163.210.1290.1441.7
3.123.1610.1280.1441.6
3.083.1210.1240.1251.5
3.043.0810.1420.1351.5
3.013.0410.1350.1181.4
2.973.0110.140.131.3
2.942.9710.1230.1081.3
2.912.9410.1160.1041.3
2.882.9110.1270.1171.2
2.852.8810.0970.0821.3
2.822.8510.0750.0561.4
2.82.8210.0670.0961.6
2.772.810.0490.0321.8
2.752.7710.0470.0271.7
2.722.7510.0440.0451.7
2.72.7210.0470.0261.8
ReflectionResolution: 2.4→50 Å / Num. obs: 68893 / % possible obs: 99.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 52.82 Å2 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.056 / Rrim(I) all: 0.104 / Χ2: 1.163 / Net I/av σ(I): 12.897 / Net I/σ(I): 7.3 / Num. measured all: 338898
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.4-2.4450.8134200.2890.8661.009100
2.44-2.49533310.40.741.005100
2.49-2.53534310.4340.5960.975100
2.53-2.59533930.5080.5240.974100
2.59-2.64534140.5880.4621.0061000.954
2.64-2.74.933950.6580.3880.9911000.7950.888
2.7-2.77533950.7680.30211000.6260.697
2.77-2.85534190.8390.2351.0441000.4830.539
2.85-2.93534600.8870.1891.0521000.3910.436
2.93-3.02533710.9090.1581.1041000.3280.365
3.02-3.13534240.9470.131.1561000.2710.302
3.13-3.26534550.9720.0961.2651000.2010.224
3.26-3.41534200.980.0771.5011000.1620.18
3.41-3.584.934240.9880.0611.4191000.1290.143
3.58-3.814.934660.9920.0461.4781000.0980.109
3.81-4.14.934730.9950.0361.31000.0780.086
4.1-4.524.934980.9960.0341.55399.80.0720.08
4.52-5.174.835100.9950.0311.5191000.0660.073
5.17-6.514.835660.9970.0241.1211000.0520.058
6.51-504.536280.9990.0150.76496.20.0320.036

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→28.991 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2391 3249 4.88 %
Rwork0.2105 --
obs0.2119 66515 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→28.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5191 0 0 237 5428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115367
X-RAY DIFFRACTIONf_angle_d1.3537330
X-RAY DIFFRACTIONf_dihedral_angle_d13.5381861
X-RAY DIFFRACTIONf_chiral_restr0.055830
X-RAY DIFFRACTIONf_plane_restr0.007965
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.43580.35291370.33222666X-RAY DIFFRACTION100
2.4358-2.47390.39441410.31332746X-RAY DIFFRACTION100
2.4739-2.51440.34891390.29572693X-RAY DIFFRACTION100
2.5144-2.55780.30891370.29652688X-RAY DIFFRACTION100
2.5578-2.60420.28821410.2862751X-RAY DIFFRACTION100
2.6042-2.65430.31791400.28252714X-RAY DIFFRACTION100
2.6543-2.70840.3041340.27932705X-RAY DIFFRACTION100
2.7084-2.76730.31741500.25412741X-RAY DIFFRACTION100
2.7673-2.83160.32361330.24072696X-RAY DIFFRACTION100
2.8316-2.90240.26711570.23232752X-RAY DIFFRACTION100
2.9024-2.98080.23551650.24092686X-RAY DIFFRACTION100
2.9808-3.06840.26651420.23792740X-RAY DIFFRACTION100
3.0684-3.16730.26951460.23342699X-RAY DIFFRACTION100
3.1673-3.28030.2481320.22362751X-RAY DIFFRACTION100
3.2803-3.41150.2731460.23152770X-RAY DIFFRACTION100
3.4115-3.56650.22141320.21372750X-RAY DIFFRACTION100
3.5665-3.75420.24151420.20562750X-RAY DIFFRACTION100
3.7542-3.98880.21071580.18972746X-RAY DIFFRACTION100
3.9888-4.29590.20241320.17642800X-RAY DIFFRACTION100
4.2959-4.72650.19731240.16572815X-RAY DIFFRACTION100
4.7265-5.40660.19751470.18482804X-RAY DIFFRACTION100
5.4066-6.79720.2421250.20782871X-RAY DIFFRACTION100
6.7972-28.99360.20131490.18082932X-RAY DIFFRACTION97

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