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- PDB-6hhv: Structure of T. thermophilus AspRS in Complex with 5'-O-(N-(L-asp... -

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Basic information

Entry
Database: PDB / ID: 6hhv
TitleStructure of T. thermophilus AspRS in Complex with 5'-O-(N-(L-aspartyl)-sulfamoyl)N3-methyluridine
ComponentsAspartate--tRNA(Asp) ligase
KeywordsLIGASE / protein-inhibitor complex / tRNA aminoacylation
Function / homology
Function and homology information


aspartate-tRNA ligase / aspartate-tRNA ligase activity / aspartyl-tRNA aminoacylation / 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 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / 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 proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
5'-O-(N-(L-aspartyl)-sulfamoyl)N3-methyluridine / Aspartate--tRNA(Asp) ligase / Aspartate--tRNA(Asp) ligase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsDe Graef, S. / Pang, L. / Strelkov, S.V. / Weeks, S.D.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders1S53518N Belgium
Research Foundation - FlandersG077814N Belgium
Research Foundation - FlandersG0A4616N Belgium
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Structural Insights into the Binding of Natural Pyrimidine-Based Inhibitors of Class II Aminoacyl-tRNA Synthetases.
Authors: Pang, L. / Nautiyal, M. / De Graef, S. / Gadakh, B. / Zorzini, V. / Economou, A. / Strelkov, S.V. / Van Aerschot, A. / Weeks, S.D.
History
DepositionAug 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 15, 2020Group: Database references / Category: citation / Item: _citation.title / _citation.year
Revision 1.3Mar 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 17, 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)133,2684
Polymers132,3642
Non-polymers9052
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10780 Å2
ΔGint-58 kcal/mol
Surface area44830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.218, 112.826, 88.533
Angle α, β, γ (deg.)90.000, 104.380, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 66181.828 Da / Num. of mol.: 2 / Fragment: aspartyl-tRNA synthetase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: aspS / Plasmid: pETRUK / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 pLysS
References: UniProt: P36419, UniProt: Q5SKD2*PLUS, aspartate-tRNA ligase
#2: Chemical ChemComp-G5Q / 5'-O-(N-(L-aspartyl)-sulfamoyl)N3-methyluridine


Mass: 452.394 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H20N4O11S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 3.01 Å3/Da / Density % sol: 59.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / 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 we caught in cryoloops and directly flash frozen in liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K
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: 2.1→67.283 Å / Num. obs: 90892 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 51.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.026 / Rrim(I) all: 0.051 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.213.90.667132860.7530.3850.77299.9
6.64-67.283.60.02729510.9980.0160.03299.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L0W

1l0w


Resolution: 2.18→67.283 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 24.75
RfactorNum. reflection% reflection
Rfree0.2255 2073 2.55 %
Rwork0.1919 --
obs0.1927 81376 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 162.37 Å2 / Biso mean: 65.1497 Å2 / Biso min: 31.34 Å2
Refinement stepCycle: final / Resolution: 2.18→67.283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8991 0 60 161 9212
Biso mean--50.65 52.52 -
Num. residues----1154
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.18-2.23070.27481410.2552685409100
2.2307-2.28650.28121230.241253085431100
2.2865-2.34830.29841390.237752625401100
2.3483-2.41740.25441330.225852635396100
2.4174-2.49550.28331370.240852695406100
2.4955-2.58470.28471350.238452705405100
2.5847-2.68820.28081260.239352935419100
2.6882-2.81050.28221600.237252585418100
2.8105-2.95870.27811390.223752965435100
2.9587-3.1440.25861610.219652455406100
3.144-3.38680.24931430.21352785421100
3.3868-3.72760.23551320.192552905422100
3.7276-4.26690.22351460.179952835429100
4.2669-5.37550.16581430.15155312545599
5.3755-67.31460.17391150.16175408552399
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)
10.9095-0.1254-0.01170.7997-0.1040.6113-0.0132-0.15790.16150.14950.1223-0.0591-0.0491-0.0042-0.10410.33530.00150.01080.318-0.01640.2794-27.0116.4401-15.8622
20.864-0.2567-0.27250.63080.16320.7574-0.032-0.0212-0.13770.08960.12280.08180.1973-0.12-0.07350.425-0.0689-0.04750.33630.05470.3518-37.1305-20.4178-20.3452
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 0 through 578)A0 - 578
2X-RAY DIFFRACTION2(chain 'B' and not resid 300:412)B0 - 300
3X-RAY DIFFRACTION2(chain 'B' and not resid 300:412)B412 - 580

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