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- PDB-7eer: Crystal structure of Tryptophanyl-tRNA synthetase from Bacillus s... -

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Basic information

Entry
Database: PDB / ID: 7eer
TitleCrystal structure of Tryptophanyl-tRNA synthetase from Bacillus stearothermophilus in complex with 05E6 and ATP
ComponentsTryptophan--tRNA ligase
KeywordsLIGASE / 05E6 / inhibitor / ANTIBIOTIC
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / ATP binding / cytosol
Similarity search - Function
Tryptophan-tRNA ligase, bacterial-type / Tryptophan-tRNA ligase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / 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
ADENOSINE-5'-TRIPHOSPHATE / 2-(1H-indol-3-yl)ethanol / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLv, G. / Fan, S. / Feng, X. / Zhang, Q. / Wu, G. / Jin, Y. / Yang, Z.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81761128016 China
National Natural Science Foundation of China (NSFC)81621064 China
Ministry of Science and Technology (MoST, China)2018YFA0901800 China
CitationJournal: To Be Published
Title: Crystal structure of Tryptophanyl-tRNA synthetase from Bacillus stearothermophilus in complex with O5E6 and ATP
Authors: Lv, G. / Fan, S. / Feng, X. / Zhang, Q. / Wu, G. / Jin, Y. / Yang, Z.
History
DepositionMar 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophan--tRNA ligase
B: Tryptophan--tRNA ligase
C: Tryptophan--tRNA ligase
D: Tryptophan--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,54512
Polymers149,8724
Non-polymers2,6748
Water0
1
A: Tryptophan--tRNA ligase
hetero molecules

A: Tryptophan--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2736
Polymers74,9362
Non-polymers1,3374
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5840 Å2
ΔGint-27 kcal/mol
Surface area25590 Å2
MethodPISA
2
B: Tryptophan--tRNA ligase
hetero molecules

B: Tryptophan--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2736
Polymers74,9362
Non-polymers1,3374
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5860 Å2
ΔGint-28 kcal/mol
Surface area25540 Å2
MethodPISA
3
C: Tryptophan--tRNA ligase
D: Tryptophan--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2736
Polymers74,9362
Non-polymers1,3374
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-25 kcal/mol
Surface area26010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.627, 87.595, 217.084
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Tryptophan--tRNA ligase / Tryptophanyl-tRNA synthetase / TrpRS


Mass: 37467.941 Da / Num. of mol.: 4 / Mutation: K64L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: trpS / Production host: Escherichia coli (E. coli) / References: UniProt: P00953, tryptophan-tRNA ligase
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-ZCW / 2-(1H-indol-3-yl)ethanol / Tryptophol


Mass: 161.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H11NO / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.78 Å3/Da / Density % sol: 50.2 % / Description: diamond
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 1.9 M K2HPO4 / PH range: 7.0-7.6

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 170735 / % possible obs: 95.1 % / Redundancy: 6 % / Biso Wilson estimate: 13.01 Å2 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.025 / Rrim(I) all: 0.064 / Χ2: 0.947 / Net I/σ(I): 7.6 / Num. measured all: 1018876
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.765.90.427165890.9270.1840.4660.95492.7
1.76-1.835.80.343165540.9430.1490.3750.96192.6
1.83-1.915.50.255164050.970.1140.280.98491.9
1.91-2.0260.186168030.9830.0790.2021.00993.7
2.02-2.1460.129167670.9890.0550.141.02493.7
2.14-2.315.80.092169900.9940.040.1011.00494.5
2.31-2.545.70.072170850.9960.0320.0790.99295.7
2.54-2.916.10.059176890.9970.0250.0640.96398.1
2.91-3.6660.038177340.9980.0170.0420.88298.2
3.66-506.70.031181190.9990.0130.0330.75799.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CKI

7cki


Resolution: 2→31.242 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2547 1238 1.17 %
Rwork0.2233 104266 -
obs0.2237 105504 95.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.54 Å2 / Biso mean: 14.3572 Å2 / Biso min: 4.4 Å2
Refinement stepCycle: final / Resolution: 2→31.242 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10360 0 172 0 10532
Biso mean--14.1 --
Num. residues----1304
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.08010.26631290.23281093390
2.0801-2.17470.21891220.23331107192
2.1747-2.28930.32041310.23641131493
2.2893-2.43270.3661380.23131124593
2.4327-2.62050.32881390.25481167096
2.6205-2.8840.24651470.26261181897
2.884-3.30090.23591370.24841196798
3.3009-4.15730.21421470.1931203398

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