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- PDB-2hz7: Crystal structure of the Glutaminyl-tRNA synthetase from Deinococ... -

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Basic information

Entry
Database: PDB / ID: 2hz7
TitleCrystal structure of the Glutaminyl-tRNA synthetase from Deinococcus radiodurans
ComponentsGlutaminyl-tRNA synthetase
KeywordsLIGASE / ROSSMANN FOLD / GLNRS CORE / CLASS I AMINOACYL-TRNA SYNTHETASE
Function / homology
Function and homology information


carbon-nitrogen ligase activity, with glutamine as amido-N-donor / glutamine-tRNA ligase / glutamine-tRNA ligase activity / glutaminyl-tRNA aminoacylation / glutamyl-tRNA aminoacylation / ATP binding / cytosol
Similarity search - Function
Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 1 / Asn/Gln amidotransferase / GatB domain / GatB domain / Aspartyl/glutamyl-tRNA amidotransferase subunit B-like / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 2 / Glutamine-tRNA ligase, bacterial / Glutamine-tRNA synthetase / Glutamine-tRNA ligase, alpha-bundle domain superfamily / Glutamyl-tRNA Synthetase; domain 2 ...Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 1 / Asn/Gln amidotransferase / GatB domain / GatB domain / Aspartyl/glutamyl-tRNA amidotransferase subunit B-like / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 2 / Glutamine-tRNA ligase, bacterial / Glutamine-tRNA synthetase / Glutamine-tRNA ligase, alpha-bundle domain superfamily / Glutamyl-tRNA Synthetase; domain 2 / Glutamyl-trna Synthetase; Domain 2 / Glutamyl-tRNA Synthetase; domain 3 / Glutamyl-tRNA Synthetase; Domain 3 / Ribosomal Protein L25; Chain P / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / Ribosomal Protein L25; Chain P / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain / HUPs / 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 / Alpha-Beta Complex / Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glutamine--tRNA ligase
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDeniziak, M. / Sauter, C. / Becker, H.D. / Paulus, C. / Giege, R. / Kern, D.
Citation
Journal: Nucleic Acids Res. / Year: 2007
Title: Deinococcus glutaminyl-tRNA synthetase is a chimer between proteins from an ancient and the modern pathways of aminoacyl-tRNA formation
Authors: Deniziak, M. / Sauter, C. / Becker, H.D. / Paulus, C.A. / Giege, R. / Kern, D.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004
Title: Crystallization and preliminary X-ray characterization of the atypical glutaminyl-tRNA synthetase from Deinococcus radiodurans
Authors: Deniziak, M. / Sauter, C. / Becker, H.D. / Giege, R. / Kern, D.
History
DepositionAug 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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

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Assembly

Deposited unit
A: Glutaminyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)93,4611
Polymers93,4611
Non-polymers00
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.1, 95.9, 115.7
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 93460.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: glnS / Plasmid: pTYB11 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: P56926, glutamine-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 7.5
Details: 4 mg/ml protein, 10% PEG 3350 and 0.1 M NaF (final concentrations) in microbatch under paraffin oil, pH 7.5, Microbatch, temperature 298K

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 20, 2004
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→29.67 Å / Num. obs: 36991 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 43.8 Å2 / Limit h max: 31 / Limit h min: 0 / Limit k max: 41 / Limit k min: 0 / Limit l max: 49 / Limit l min: 0 / Observed criterion F max: 2034717.51 / Observed criterion F min: 4.7 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Χ2: 1.342 / Net I/σ(I): 18.1
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 5.5 / Num. unique all: 2635 / Rsym value: 0.25 / Χ2: 1.574 / % possible all: 92.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
DNAdata collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O0B

1o0b


Resolution: 2.3→29.67 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2612 7.1 %RANDOM
Rwork0.2 ---
all0.2 37336 --
obs0.2 36654 98.2 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 27.7546 Å2 / ksol: 0.316668 e/Å3
Displacement parametersBiso max: 100.27 Å2 / Biso mean: 41.68 Å2 / Biso min: 17.73 Å2
Baniso -1Baniso -2Baniso -3
1-8.91 Å20 Å20 Å2
2---15 Å20 Å2
3---6.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.23 Å
Luzzati d res high-2.3
Refinement stepCycle: LAST / Resolution: 2.3→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4488 0 0 160 4648
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_mcbond_it1.962
X-RAY DIFFRACTIONc_mcangle_it2.913
X-RAY DIFFRACTIONc_scbond_it4.012.5
X-RAY DIFFRACTIONc_scangle_it5.634
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.3-2.360.2931957.40.25524330.0212839262892.5
2.36-2.430.3212027.50.24124960.0232836269895.1
2.43-2.510.3151766.30.25426180.0242858279497.7
2.51-2.60.2951957.10.23925640.0212817275997.9
2.6-2.70.2772117.60.23625750.0192843278698
2.7-2.830.281615.80.24326340.0222853279598
2.83-2.980.3131906.80.24725970.0232843278798
2.98-3.160.28719770.2326300.022858282798.9
3.16-3.410.2542107.40.21226420.0182876285299.1
3.41-3.750.22822880.20426330.0152869286199.7
3.75-4.290.22207.60.1726850.0132909290599.9
4.29-5.40.1922036.90.15327210.0132925292499.9
5.4-29.670.2282247.40.17828140.0153060303899.2
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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