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- PDB-5bnz: Crystal structure of Glutamine-tRNA ligase /Glutaminyl-tRNA synth... -

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Basic information

Entry
Database: PDB / ID: 5bnz
TitleCrystal structure of Glutamine-tRNA ligase /Glutaminyl-tRNA synthetase (GlnRS) from Pseudomonas aeruginosa
ComponentsGlutamine--tRNA ligase
KeywordsLIGASE / SSGCID / Pseudomonas aeruginosa / Glutamine--tRNA ligase / Glutaminyl-tRNA synthetase (GlnRS) / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


glutamine-tRNA ligase / glutamine-tRNA ligase activity / glutaminyl-tRNA aminoacylation / glutamyl-tRNA aminoacylation / ATP binding / cytosol
Similarity search - Function
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 ...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 / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / 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 speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of Glutamine-tRNA ligase /Glutaminyl-tRNA synthetase (GlnRS) from Pseudomonas aeruginosa
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionMay 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description ...Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_struct_assembly ...entity_src_gen / pdbx_struct_assembly / pdbx_struct_oper_list / software / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: Glutamine--tRNA ligase
B: Glutamine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,5138
Polymers128,0582
Non-polymers4556
Water27,2751514
1
A: Glutamine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2564
Polymers64,0291
Non-polymers2283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutamine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2564
Polymers64,0291
Non-polymers2283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.010, 56.020, 127.140
Angle α, β, γ (deg.)90.000, 99.410, 90.000
Int Tables number3
Space group name H-MP121

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Components

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


Mass: 64028.918 Da / Num. of mol.: 2 / Fragment: PsaeA.18222.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: glnS, PA1794 / Plasmid: PsaeA.18222.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I2U8, glutamine-tRNA ligase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1514 / 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: 2.99 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: Microlytics , MCSG1 C2 opt: 100mM BisTris pH 6.5, 200mM Lithium-sulphate, 23% PEG 3350; PsaeA.18222.a.B1.PW37623 at 20 mg/ml + 2.5mM AMPPNP and MgCl2; cryo: 20% EG + AMPPNP/Gln in two steps; ...Details: Microlytics , MCSG1 C2 opt: 100mM BisTris pH 6.5, 200mM Lithium-sulphate, 23% PEG 3350; PsaeA.18222.a.B1.PW37623 at 20 mg/ml + 2.5mM AMPPNP and MgCl2; cryo: 20% EG + AMPPNP/Gln in two steps; tray 262504b8, puck bfw9-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 26, 2015
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 119957 / Num. obs: 119747 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 11.71
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 5 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 3.31 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
BALBESphasing
RESOLVEmodel building
Cootmodel building
PHENIXphasing
PHENIXdev_2027refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1nyl

1nyl


Resolution: 1.9→41.809 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2282 1999 1.67 %Random selection
Rwork0.1876 117728 --
obs0.1883 119727 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.37 Å2 / Biso mean: 22.6515 Å2 / Biso min: 7.29 Å2
Refinement stepCycle: final / Resolution: 1.9→41.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8607 0 22 1522 10151
Biso mean--52.37 32.31 -
Num. residues----1096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079002
X-RAY DIFFRACTIONf_angle_d1.00612250
X-RAY DIFFRACTIONf_chiral_restr0.0481271
X-RAY DIFFRACTIONf_plane_restr0.0051654
X-RAY DIFFRACTIONf_dihedral_angle_d13.4663380
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.94750.27591420.232883398481100
1.9475-2.00020.28791420.226283448486100
2.0002-2.0590.29891410.21783428483100
2.059-2.12550.25321430.206583638506100
2.1255-2.20140.2371410.206883648505100
2.2014-2.28960.27571430.19983508493100
2.2896-2.39380.23211410.190283898530100
2.3938-2.520.2351430.193783898532100
2.52-2.67780.25091440.195284238567100
2.6778-2.88450.21251420.190183708512100
2.8845-3.17470.22231420.184184488590100
3.1747-3.63390.21971450.171484548599100
3.6339-4.57740.18641430.154684908633100
4.5774-41.81960.20171470.18478663881099
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2435-0.05220.22981.32950.57281.9160.02290.0502-0.0532-0.13720.01660.1090.0185-0.0193-0.03250.1022-0.01870.00030.09720.02750.0881147.8957-0.284743.3317
20.58980.8550.14172.54030.21140.2384-0.0764-0.01820.1139-0.38330.02740.2352-0.0396-0.06580.02920.1659-0.0155-0.01220.1383-0.00560.0987153.067522.993535.5398
30.23290.0634-0.65190.5946-0.55432.03840.00240.05620.0214-0.13390.09370.1217-0.08-0.1807-0.08990.1086-0.0213-0.02320.16120.03080.1418135.90830.70651.7064
41.56230.9539-1.01751.3411-0.75921.5303-0.0020.07490.03780.04110.02790.16720.082-0.05570.02140.1273-0.00910.04350.10960.03040.1577122.6309-23.72979.4561
50.7562-0.1078-0.12482.8319-0.41561.4488-0.00510.12890.1699-0.05760.05280.2036-0.0917-0.1661-0.03020.0793-0.01750.01880.16260.05950.1731130.8749-5.276467.363
61.41540.54420.2611.54610.33741.7671-0.0553-0.0499-0.00330.07440.0411-0.1592-0.0720.08660.020.09680.035-0.00120.0949-0.01160.104127.9823-10.66495.9898
70.25260.08290.17262.64360.84590.72780.011-0.0778-0.02880.27420.0712-0.33590.12490.0107-0.060.10730.0036-0.02260.1364-0.02740.1601136.1204-33.73770.9529
81.3541-0.4898-0.32850.46860.23980.3239-0.0525-0.12770.0060.12690.0592-0.13760.04640.02620.00510.15350.0318-0.02620.1579-0.01660.1119119.3322-11.407117.6968
91.5016-0.8461-1.06741.48750.91311.6869-0.0029-0.04350.13990.15150.04140.06430.02170.0324-0.06160.14730.03640.03990.1112-0.00650.130591.228312.994629.9055
101.4693-0.41310.05462.1506-0.18490.8156-0.0255-0.1748-0.06510.15830.04810.00340.15190.1027-0.0080.16570.05330.02210.1602-0.01590.0759103.5856-5.514822.0334
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 100 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 101 through 248 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 249 through 340 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 341 through 473 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 474 through 555 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 8 through 100 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 101 through 248 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 249 through 340 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 341 through 473 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 474 through 555 )B0

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