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

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Basic information

Entry
Database: PDB / ID: 6hhx
TitleStructure of T. thermophilus AspRS in Complex with 5'-O-(N-(L-aspartyl)-sulfamoyl)cytidine
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)cytidine / Aspartate--tRNA(Asp) ligase / Aspartate--tRNA(Asp) ligase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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

Downloads & links

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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)133,2384
Polymers132,3642
Non-polymers8752
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10760 Å2
ΔGint-59 kcal/mol
Surface area44780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.123, 112.706, 88.679
Angle α, β, γ (deg.)90.000, 104.400, 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-G5N / 5'-O-(N-(L-aspartyl)-sulfamoyl)cytidine


Mass: 437.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N5O10S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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 Å3/Da / Density % sol: 59.04 %
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: 2.03→68.32 Å / Num. obs: 100487 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 47.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.025 / Rrim(I) all: 0.064 / Net I/σ(I): 14.9 / Num. measured all: 681569
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.03-2.1470.886146650.7670.360.957100
6.43-68.326.40.03832660.9990.0160.04199.7

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Processing

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

1l0w


Resolution: 2.1→57.78 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 24.67
RfactorNum. reflection% reflection
Rfree0.2178 2103 2.31 %
Rwork0.1881 --
obs0.1888 91110 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 155 Å2 / Biso mean: 61.4528 Å2 / Biso min: 28.14 Å2
Refinement stepCycle: final / Resolution: 2.1→57.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8993 0 58 162 9213
Biso mean--47.95 49.02 -
Num. residues----1154
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1-2.14890.30471470.243859496096
2.1489-2.20260.28121200.229259266046
2.2026-2.26220.25671320.229658836015
2.2622-2.32870.27441430.215259506093
2.3287-2.40390.25331400.21659316071
2.4039-2.48980.24531370.221459026039
2.4898-2.58950.27751230.226959056028
2.5895-2.70730.25431200.22959686088
2.7073-2.85010.26551200.240759486068
2.8501-3.02860.30161500.224959096059
3.0286-3.26250.24291580.217359246082
3.2625-3.59070.22661560.19959146070
3.5907-4.11020.2171270.175959536080
4.1102-5.17790.17511830.147259306113
5.1779-57.80190.17361470.155360156162
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)
11.0721-0.13810.00720.8036-0.13760.5695-0.0088-0.16090.17660.13090.1147-0.0482-0.0356-0.0246-0.10170.36380.00320.0110.3549-0.01560.31-26.99616.5321-15.859
21.0019-0.1728-0.36280.5860.160.7281-0.0152-0.0308-0.14150.05960.10550.08180.1956-0.1116-0.07750.4042-0.0631-0.05840.3270.06180.3389-37.1113-20.3043-20.3328
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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