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- PDB-6brl: Crystal structure of a glutamate tRNA ligase from Elizabethkingia... -

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Basic information

Entry
Database: PDB / ID: 6brl
TitleCrystal structure of a glutamate tRNA ligase from Elizabethkingia meningosepticum CCUG26117 in complex with its amino acid
ComponentsGlutamate tRNA ligase
KeywordsLIGASE / SSGCID / Chryseobacterium / Flavobacterium / 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 / cytoplasm
Similarity search - Function
Glutamate-tRNA ligase, bacterial/mitochondrial / Aminoacyl-tRNA synthetase, class I, anticodon-binding domain, subdomain 2 / Glutamyl-tRNA synthetase / Anticodon binding domain / Aminoacyl-tRNA synthetase, class I, anticodon-binding superfamily / Glutamyl-tRNA Synthetase; domain 2 / Glutamyl-trna Synthetase; Domain 2 / Glutamyl-tRNA Synthetase; domain 3 / Glutamyl-tRNA Synthetase; Domain 3 / Glutamyl/glutaminyl-tRNA synthetase ...Glutamate-tRNA ligase, bacterial/mitochondrial / Aminoacyl-tRNA synthetase, class I, anticodon-binding domain, subdomain 2 / Glutamyl-tRNA synthetase / Anticodon binding domain / Aminoacyl-tRNA synthetase, class I, anticodon-binding superfamily / Glutamyl-tRNA Synthetase; domain 2 / Glutamyl-trna Synthetase; Domain 2 / Glutamyl-tRNA Synthetase; domain 3 / Glutamyl-tRNA Synthetase; Domain 3 / 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 / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / Glutamate--tRNA ligase
Similarity search - Component
Biological speciesElizabethkingia meningoseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Crystal structures of glutamyl-tRNA synthetase from Elizabethkingia anopheles and E. meningosepticum.
Authors: Brooks, L. / Subramanian, S. / Dranow, D.M. / Mayclin, S.J. / Myler, P.J. / Asojo, O.A.
History
DepositionNov 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
Revision 1.2Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9605
Polymers58,6271
Non-polymers3334
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.260, 111.890, 130.170
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


Mass: 58626.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia meningoseptica (bacteria)
Strain: CCUG 26117 / Plasmid: ElmeA.01348.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1T3HI54*PLUS
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MCSG1 E10 (295949e10): 200mM Ammonium tartarate dibasic, 20% (w/v) PEG3350: ElmeA.01348.a.B1.PW38364 16.23 mg/mL, direct cryo: xxk4-10

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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: Nov 16, 2017
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→35.854 Å / Num. obs: 43563 / % possible obs: 99.8 % / Redundancy: 6.092 % / Biso Wilson estimate: 31.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.069 / Χ2: 1.009 / Net I/σ(I): 17.75
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.056.1750.5723.2131690.8840.62499.9
2.05-2.116.180.4554.0530990.9010.496100
2.11-2.176.1460.3675.0130280.9380.4100
2.17-2.246.2040.2856.2829030.9660.311100
2.24-2.316.1530.2427.3928460.9740.264100
2.31-2.396.1940.1969.0327710.9810.214100
2.39-2.486.1560.15910.8226420.9870.173100
2.48-2.586.1270.13312.5825610.9910.145100
2.58-2.76.1450.11115.1824760.9930.12199.9
2.7-2.836.1490.08918.1923680.9960.097100
2.83-2.986.1070.07222.0922350.9970.07899.8
2.98-3.166.0780.05925.8121540.9970.065100
3.16-3.386.0310.04930.8920000.9980.05399.7
3.38-3.656.0470.04334.7118830.9980.04699.8
3.65-46.0160.03838.3117470.9990.04199.6
4-4.475.990.03540.7515730.9980.03899.6
4.47-5.165.9450.03341.2513950.9990.03699.5
5.16-6.325.8320.03338.8912170.9990.03699.2
6.32-8.945.7110.03141.169440.9990.03498.8
8.94-35.8544.9710.02940.945520.9990.03295.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.31 Å42.43 Å
Translation5.31 Å42.43 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASER2.7.17phasing
PHENIX(dev_2947)refinement
PDB_EXTRACT3.24data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GRI, 2JA2, and 2WMX

4gri

2ja2

2wmx


Resolution: 2→35.854 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.89
RfactorNum. reflection% reflection
Rfree0.2139 1997 4.59 %
Rwork0.1683 --
obs0.1705 43551 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 96.17 Å2 / Biso mean: 37.4443 Å2 / Biso min: 17.04 Å2
Refinement stepCycle: final / Resolution: 2→35.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3947 0 22 404 4373
Biso mean--50.85 44.46 -
Num. residues----502
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0001-2.05010.25471360.212829223058100
2.0501-2.10550.26881360.199729263062100
2.1055-2.16750.23951610.19529183079100
2.1675-2.23740.22951340.18629223056100
2.2374-2.31740.25271350.181729463081100
2.3174-2.41010.22911160.181529793095100
2.4101-2.51980.23251230.174829483071100
2.5198-2.65260.23251490.181329333082100
2.6526-2.81870.26421530.186629503103100
2.8187-3.03630.25481510.189829603111100
3.0363-3.34160.2391620.187129823144100
3.3416-3.82470.21371300.163630043134100
3.8247-4.81690.16591470.129830373184100
4.8169-35.85970.17241640.15323127329199
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)
11.0708-0.66130.57931.6262-1.07881.415-0.02860.082-0.01440.03420.04330.0653-0.0428-0.0453-0.02940.1347-0.0256-0.00560.2167-0.0250.192230.847100.65540.589
20.1218-0.65730.20754.6308-1.16190.61450.07470.02970.0038-0.1308-0.1584-0.07480.2110.03440.08180.2639-0.0205-0.01040.28570.00880.222245.45463.84352.717
38.01673.11825.76411.92822.20054.1468-0.07290.2652-0.6263-0.61780.2929-0.17840.3366-0.2937-0.21520.5627-0.11320.05180.6502-0.09650.552435.31493.29844.043
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:200 )A2 - 200
2X-RAY DIFFRACTION2( CHAIN A AND RESID 201:502 )A201 - 502
3X-RAY DIFFRACTION3( CHAIN A AND RESID 601:601 )A601

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