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- PDB-5tgt: Crystal structure of glytamyl-tRNA synthetase GluRS from Pseudomo... -

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Basic information

Entry
Database: PDB / ID: 5tgt
TitleCrystal structure of glytamyl-tRNA synthetase GluRS from Pseudomonas aeruginosa
ComponentsGlutamate--tRNA ligase
KeywordsLIGASE / SSGCID / glutamyl-tRNA synthetase / GluRS / Pseudomonas aeruginosa / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / tRNA binding / zinc ion binding / ATP binding / cytosol
Similarity search - Function
Arc Repressor Mutant, subunit A - #350 / Glutamate-tRNA ligase, bacterial/mitochondrial / Glutamyl-tRNA synthetase / : / Aminoacyl-tRNA synthetase, class I, anticodon-binding superfamily / Aminoacyl-tRNA synthetase, class I, anticodon-binding domain, subdomain 2 / Aminoacyl-tRNA synthetase, class I, anticodon-binding / Anticodon binding domain / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain ...Arc Repressor Mutant, subunit A - #350 / Glutamate-tRNA ligase, bacterial/mitochondrial / Glutamyl-tRNA synthetase / : / Aminoacyl-tRNA synthetase, class I, anticodon-binding superfamily / Aminoacyl-tRNA synthetase, class I, anticodon-binding domain, subdomain 2 / Aminoacyl-tRNA synthetase, class I, anticodon-binding / Anticodon 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. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Arc Repressor Mutant, subunit A / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glutamate--tRNA ligase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of glytamyl-tRNA synthetase GluRS from Pseudomonas aeruginosa
Authors: Mayclin, S.J. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionSep 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)117,47017
Polymers115,7152
Non-polymers1,75515
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-194 kcal/mol
Surface area41550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.840, 138.660, 202.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glutamate--tRNA ligase / Glutamyl-tRNA synthetase / GluRS


Mass: 57857.371 Da / Num. of mol.: 2 / Fragment: PsaeA.01348.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: gltX, PA3134 / Plasmid: PsaeA.01348.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9XCL6, glutamate-tRNA ligase
#2: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.84 Å3/Da / Density % sol: 57 % / Mosaicity: 0.18 °
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: JCSG+ D9(271290d9): 170mM Ammonium Sulfate, 25.5% w/v PEG4000 15% v/v glycerol, 2mM BSI100156; dc; 24mg/mL; dkp0-3

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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-300 / Detector: CCD / Date: Apr 13, 2016
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.45→45.061 Å / Num. obs: 49576 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 47.01 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.065 / Χ2: 0.983 / Net I/σ(I): 19.61 / Num. measured all: 303206
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.45-2.510.4963.5422154356435640.8990.541100
2.51-2.580.44.3722072354135400.9290.436100
2.58-2.660.3395.1721408344234400.9440.3799.9
2.66-2.740.2716.4420851333333330.9610.295100
2.74-2.830.218.0819859320532040.9750.229100
2.83-2.930.1739.6119820318531840.9840.189100
2.93-3.040.1411.6218571298829860.9890.15399.9
3.04-3.160.10415.1218122293229300.9940.11399.9
3.16-3.30.08418.517273279127870.9950.09199.9
3.3-3.460.06722.2916605269126900.9970.073100
3.46-3.650.05426.9715836257825760.9980.05999.9
3.65-3.870.04631.3714818242524220.9980.05199.9
3.87-4.140.04334.5413671227022670.9980.04799.9
4.14-4.470.03938.0512863215121510.9990.042100
4.47-4.90.03641.0611784197919770.9980.0499.9
4.9-5.480.03739.3410712181418140.9990.041100
5.48-6.330.03638.449450160616050.9990.0499.9
6.33-7.750.03142.568115139713920.9990.03399.6
7.75-10.960.02546.486063108410810.9990.02799.7
10.960.02444.7631596596330.9990.02796.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GRI

4gri


Resolution: 2.45→45.061 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2296 1976 3.99 %
Rwork0.1835 47594 -
obs0.1853 49570 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.8 Å2 / Biso mean: 55.4079 Å2 / Biso min: 27.49 Å2
Refinement stepCycle: final / Resolution: 2.45→45.061 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6927 0 99 104 7130
Biso mean--92.93 49.28 -
Num. residues----914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087247
X-RAY DIFFRACTIONf_angle_d1.0679891
X-RAY DIFFRACTIONf_chiral_restr0.0441078
X-RAY DIFFRACTIONf_plane_restr0.0061279
X-RAY DIFFRACTIONf_dihedral_angle_d17.8134250
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 (%)
2.45-2.51130.28961260.224333153441100
2.5113-2.57920.2561390.203733683507100
2.5792-2.65510.27261480.20733343482100
2.6551-2.74080.2651440.207233643508100
2.7408-2.83870.26381420.199633283470100
2.8387-2.95240.25131330.200233823515100
2.9524-3.08670.22711380.197433753513100
3.0867-3.24940.28521470.197933613508100
3.2494-3.45290.28381320.197733783510100
3.4529-3.71940.21981370.180334163553100
3.7194-4.09350.21651390.167434223561100
4.0935-4.68530.19631660.150434423608100
4.6853-5.90080.18771420.181534603602100
5.9008-45.06820.22441430.18493649379299
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)
10.6955-0.8913-0.88062.5936-0.04771.9148-0.0415-0.03240.27480.19080.00380.20140.1589-0.132-0.00120.4542-0.0132-0.01610.5322-0.12920.441546.43161.68941.456
22.3007-0.0791-0.42060.7080.17510.04810.21750.09110.9129-0.1005-0.13370.25620.0224-0.02850.00020.51740.03690.03370.5487-0.12960.898734.27781.67840.561
30.8277-0.3711-0.18363.27030.63090.26650.0438-0.09620.4749-0.13050.0185-0.326-0.05570.06320.00020.4702-0.0094-0.0080.5098-0.08140.470353.97760.53733.715
40.9603-0.8376-0.29631.8769-1.55221.52780.0264-0.0060.0247-0.10480.20860.4141-0.1093-0.24760.00350.42420.0274-0.04330.4452-0.01110.365134.4644.16917.606
51.45010.79460.05862.4321-0.45920.5009-0.01580.0818-0.5409-0.06140.13890.34040.0502-0.06160.00070.5085-0.00320.03340.4772-0.13010.673333.51857.95169.43
61.10340.2870.11832.2288-0.0414-0.07-0.0013-0.0367-0.50660.15380.0279-0.18330.09350.01320.00060.5389-0.00950.03290.4898-0.02510.471842.1568.60177.556
72.09860.3101-0.1041.6104-0.32962.9560.0594-0.0731-0.11880.06920.13310.32220.1569-0.50190.00040.4393-0.03720.03810.42920.00050.37325.50186.40789.248
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 10:73 )A10 - 73
2X-RAY DIFFRACTION2( CHAIN A AND RESID 74:202 )A74 - 202
3X-RAY DIFFRACTION3( CHAIN A AND RESID 203:349 )A203 - 349
4X-RAY DIFFRACTION4( CHAIN A AND RESID 350:493 )A350 - 493
5X-RAY DIFFRACTION5( CHAIN B AND RESID 11:146 )B11 - 146
6X-RAY DIFFRACTION6( CHAIN B AND RESID 147:381 )B147 - 381
7X-RAY DIFFRACTION7( CHAIN B AND RESID 382:493 )B382 - 493

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