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- PDB-7k86: Crystal Structure of Glutamyl-tRNA synthetase (gltX) from Stenotr... -

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Basic information

Entry
Database: PDB / ID: 7k86
TitleCrystal Structure of Glutamyl-tRNA synthetase (gltX) from Stenotrophomonas maltophilia
ComponentsGlutamate--tRNA ligase
KeywordsLIGASE / SSGCID / Stenotrophomonas maltophilia K279a / Stenotrophomonas / gltX / Glutamyl-tRNA synthetase / 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/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
Similarity search - Domain/homology
ACETATE ION / Glutamate--tRNA ligase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Glutamyl-tRNA synthetase (gltX) from Stenotrophomonas maltophilia
Authors: Dranow, D.M. / Davies, D.R. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionSep 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Glutamate--tRNA ligase
B: Glutamate--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,4738
Polymers106,1062
Non-polymers3666
Water6,828379
1
A: Glutamate--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2985
Polymers53,0531
Non-polymers2454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutamate--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1743
Polymers53,0531
Non-polymers1212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.400, 69.110, 103.820
Angle α, β, γ (deg.)90.000, 110.060, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 53053.105 Da / Num. of mol.: 2 / Fragment: StmaA.01187.b.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria)
Strain: K279a / Gene: gltX, Smlt1441 / Plasmid: StmaA.01187.b.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2FHI7, glutamate-tRNA ligase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 51.6 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: StmaA.01187.b.B1.PW38726 at 24 mg/ml mixed 1:1 with MCSG1(c5): 10%(w/v) PEG-3350, 0.2 M magensium acetate. Tray: 313794c5. Puck: xku5-10.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 5, 2020 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.05→36.26 Å / Num. obs: 71304 / % possible obs: 99.6 % / Redundancy: 4.12 % / Biso Wilson estimate: 47.788 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.045 / Χ2: 1.032 / Net I/σ(I): 18.49 / Num. measured all: 293786 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.05-2.13.230.4342.4216429522150870.8740.52397.4
2.1-2.163.9060.353.5420129516151540.9480.40699.9
2.16-2.224.2470.2684.8121154498749810.9720.30699.9
2.22-2.294.2460.2136.0220502484048290.9820.24499.8
2.29-2.374.2580.1687.5520000470046970.9870.19299.9
2.37-2.454.2550.1369.1219337455645450.9910.15599.8
2.45-2.544.2450.10711.1818693441044040.9940.12399.9
2.54-2.654.2650.08713.7917862419441880.9960.199.9
2.65-2.764.2510.07316.2317336408840780.9960.08499.8
2.76-2.94.2340.05919.5516390387638710.9980.06799.9
2.9-3.064.2240.04823.8915674371637110.9980.05599.9
3.06-3.244.2150.04128.0514657347934770.9980.04699.9
3.24-3.474.1920.03532.9613860331233060.9990.0499.8
3.47-3.744.1760.03137.2312677303830360.9990.03599.9
3.74-4.14.1620.02939.6311828284828420.9990.03399.8
4.1-4.584.1540.02742.3210677257425700.9990.03199.8
4.58-5.294.1410.02542.579391227122680.9990.02999.9
5.29-6.484.1250.02741.867977193919340.9990.03199.7
6.48-9.174.0850.02443.996128150615000.9990.02799.6
9.17-36.263.7350.02543.4730858588260.9980.0396.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H4V

5h4v


Resolution: 2.05→36.26 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2282 1889 2.65 %
Rwork0.1821 69364 -
obs0.1833 71253 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.52 Å2 / Biso mean: 53.6355 Å2 / Biso min: 29.56 Å2
Refinement stepCycle: final / Resolution: 2.05→36.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7137 0 24 380 7541
Biso mean--54.99 51.43 -
Num. residues----923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067365
X-RAY DIFFRACTIONf_angle_d0.80210016
X-RAY DIFFRACTIONf_dihedral_angle_d17.4892700
X-RAY DIFFRACTIONf_chiral_restr0.0461114
X-RAY DIFFRACTIONf_plane_restr0.0051323
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.110.32261370.28245167530497
2.11-2.170.28581470.242653195466100
2.17-2.240.30621460.219653185464100
2.24-2.320.29941530.214553035456100
2.32-2.410.29921480.213253055453100
2.41-2.520.28831330.213553305463100
2.52-2.650.27191510.208253425493100
2.65-2.820.26591380.21253435481100
2.82-3.040.24061510.208453235474100
3.04-3.340.25621420.197253655507100
3.34-3.820.21441660.179753495515100
3.82-4.820.16561420.14454045546100
4.82-36.260.20061350.15295496563199
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)
11.3487-0.391-0.10870.88280.84266.83920.18270.37330.1484-0.2949-0.0905-0.0407-0.2516-0.5369-0.0760.3608-0.00750.04310.4197-0.00580.3396-15.3956-0.4791-2.2134
23.4180.40113.66870.19470.48155.1094-0.16160.14-0.07350.0030.1349-0.1229-0.1910.15160.03650.3581-0.01740.0370.2784-0.10210.45855.46996.475737.0684
31.74320.14390.14151.4953-1.02134.0823-0.0118-0.13220.17710.2058-0.0790.0059-0.28870.05050.08660.279-0.03070.00550.34510.03680.333443.39910.513639.5488
43.8063-0.76062.62.1584-0.72515.54260.43250.0461-0.5798-0.4674-0.10410.18370.5361-0.1862-0.31310.53720.013-0.10740.38230.07210.454418.27425.4678-3.5769
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 217 )A1 - 217
2X-RAY DIFFRACTION2chain 'A' and (resid 218 through 465 )A218 - 465
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 299 )B1 - 299
4X-RAY DIFFRACTION4chain 'B' and (resid 300 through 464 )B300 - 464

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