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- PDB-7ap4: Thermus thermophilus Aspartyl-tRNA Synthetase in Complex with Com... -

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Basic information

Entry
Database: PDB / ID: 7ap4
TitleThermus thermophilus Aspartyl-tRNA Synthetase in Complex with Compound AspS7HMDDA
ComponentsAspartate--tRNA(Asp) ligase
KeywordsLIGASE / protein-inhibitor complex / tRNA aminoacylation
Function / homology
Function and homology information


aspartate-tRNA ligase / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / nucleic acid binding / ATP binding / cytoplasm
Similarity search - Function
: / : / Aspartate-tRNA ligase, type 1 / GAD domain / GAD domain / GAD-like domain superfamily / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type ...: / : / Aspartate-tRNA ligase, type 1 / GAD domain / GAD domain / GAD-like domain superfamily / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Chem-RSN / Aspartate--tRNA(Asp) ligase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsDe Graef, S. / Pang, L. / Strelkov, S.V. / Weeks, S.D.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1S53518N Belgium
CitationJournal: Molecules / Year: 2020
Title: Synthesis and Biological Evaluation of 1,3-Dideazapurine-Like 7-Amino-5-Hydroxymethyl-Benzimidazole Ribonucleoside Analogues as Aminoacyl-tRNA Synthetase Inhibitors.
Authors: Zhang, B. / Pang, L. / Nautiyal, M. / De Graef, S. / Gadakh, B. / Lescrinier, E. / Rozenski, J. / Strelkov, S.V. / Weeks, S.D. / Van Aerschot, A.
History
DepositionOct 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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

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Assembly

Deposited unit
A: Aspartate--tRNA(Asp) ligase
B: Aspartate--tRNA(Asp) ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,3434
Polymers132,3642
Non-polymers9792
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
  • dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10890 Å2
ΔGint-55 kcal/mol
Surface area45130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.277, 112.531, 88.253
Angle α, β, γ (deg.)90.000, 104.860, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aspartate--tRNA(Asp) ligase / Aspartyl-tRNA synthetase 1 / AspRS1 / Discriminating aspartyl-tRNA synthetase / D-AspRS


Mass: 66181.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: aspS1, TTHA0711 / Plasmid: pETRUK / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rossetta 2 (DE3) pLysS / References: UniProt: Q5SKD2, aspartate-tRNA ligase
#2: Chemical ChemComp-RSN / (3~{S})-3-azanyl-4-[[(2~{R},3~{S},4~{R},5~{R})-5-[7-azanyl-5-(hydroxymethyl)benzimidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxysulfonylamino]-4-oxidanylidene-butanoic acid


Mass: 489.457 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H23N5O10S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O
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: 3.01 Å3/Da / Density % sol: 59.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: A 10 mg/ml protein solution was prepared in 10 mM TRIS pH 7.5, 100 mM NaCl, 2.5 mM DTT and 0.4% w/v low melting point agarose, maintaining the sample temperature at 315 kelvin. Crystals were ...Details: A 10 mg/ml protein solution was prepared in 10 mM TRIS pH 7.5, 100 mM NaCl, 2.5 mM DTT and 0.4% w/v low melting point agarose, maintaining the sample temperature at 315 kelvin. Crystals were grown by mixing an equal volume of the protein solution with 8-12% PEG 4000, 0.1 M Morpheus buffer system 1 (MES/imidazole) pH 7, 100 mM KCl, 20 v/v % glycerol. For soaking a 4 mM solution of compound in DMSO was used. A one third volume of the initial drop size was pipetted carefully onto the crystal containing drop. The sample was then placed back over the reservoir and incubated for approximately 2 hr. Crystals were caught in cryoloops and directly flash frozen in liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 2.06→79.53 Å / Num. obs: 94888 / % possible obs: 99 % / Redundancy: 3.8 % / Biso Wilson estimate: 47.89 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.041 / Rrim(I) all: 0.082 / Net I/σ(I): 9.5 / Num. measured all: 356281 / Scaling rejects: 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.06-2.173.90.69953328138110.7410.4010.8081.798.6
6.51-79.533.60.0511104130830.9960.030.05921.498.7

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L0W

1l0w


Resolution: 2.15→79.526 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 26.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2405 2055 2.46 %
Rwork0.1985 81361 -
obs0.1995 83416 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 553.7 Å2 / Biso mean: 70.5674 Å2 / Biso min: 30.07 Å2
Refinement stepCycle: final / Resolution: 2.15→79.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8953 0 110 297 9360
Biso mean--73.46 53.11 -
Num. residues----1153
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.15-2.20.31251450.2797537499
2.2-2.2550.28881570.2667537699
2.255-2.3160.30151500.2516535198
2.316-2.38420.29721380.2497537599
2.3842-2.46110.27741030.2412544899
2.4611-2.54910.30431380.2356541999
2.5491-2.65120.27991250.2344541399
2.6512-2.77180.25921160.2354542799
2.7718-2.9180.26831550.2339541999
2.918-3.10080.25871530.229538499
3.1008-3.34020.25331370.2136546599
3.3402-3.67640.23971490.1978545599
3.6764-4.20830.21021240.1772545399
4.2083-5.30190.20591310.1524546199
5.3019-79.5260.21661340.182554199

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