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Yorodumi- PDB-8ahw: Structure of DCS-resistant variant D322N of alanine racemase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ahw | ||||||||||||||||||
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Title | Structure of DCS-resistant variant D322N of alanine racemase from Mycobacterium tuberculosis | ||||||||||||||||||
Components | Alanine racemase | ||||||||||||||||||
Keywords | ISOMERASE / Enzyme / alanine racemase / peptidoglycan biosynthesis | ||||||||||||||||||
Function / homology | Function and homology information alanine racemase / D-alanine biosynthetic process / alanine racemase activity / peptidoglycan biosynthetic process / pyridoxal phosphate binding / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||||||||||||||
Authors | de Chiara, C. / Prosser, G. / Ogrodowicz, R.W. / de Carvalho, L.P.S. | ||||||||||||||||||
Funding support | United Kingdom, 5items
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Citation | Journal: Acs Bio Med Chem Au / Year: 2023 Title: Structure of the d-Cycloserine-Resistant Variant D322N of Alanine Racemase from Mycobacterium tuberculosis . Authors: de Chiara, C. / Prosser, G.A. / Ogrodowicz, R. / de Carvalho, L.P.S. #1: Journal: Nat Commun / Year: 2019 Title: Comparative fitness analysis of D-cycloserine resistant mutants reveals both fitness-neutral and high-fitness cost genotypes. Authors: Evangelopoulos, D. / Prosser, G.A. / Rodgers, A. / Dagg, B.M. / Khatri, B. / Ho, M.M. / Gutierrez, M.G. / Cortes, T. / de Carvalho, L.P.S. #2: Journal: Nat Chem Biol / Year: 2020 Title: D-Cycloserine destruction by alanine racemase and the limit of irreversible inhibition. Authors: de Chiara, C. / Homsak, M. / Prosser, G.A. / Douglas, H.L. / Garza-Garcia, A. / Kelly, G. / Purkiss, A.G. / Tate, E.W. / de Carvalho, L.P.S. #3: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. #4: Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Authors: Liebschner, D. / Afonine, P.V. / Baker, M.L. / Bunkoczi, G. / Chen, V.B. / Croll, T.I. / Hintze, B. / Hung, L.W. / Jain, S. / McCoy, A.J. / Moriarty, N.W. / Oeffner, R.D. / Poon, B.K. / ...Authors: Liebschner, D. / Afonine, P.V. / Baker, M.L. / Bunkoczi, G. / Chen, V.B. / Croll, T.I. / Hintze, B. / Hung, L.W. / Jain, S. / McCoy, A.J. / Moriarty, N.W. / Oeffner, R.D. / Poon, B.K. / Prisant, M.G. / Read, R.J. / Richardson, J.S. / Richardson, D.C. / Sammito, M.D. / Sobolev, O.V. / Stockwell, D.H. / Terwilliger, T.C. / Urzhumtsev, A.G. / Videau, L.L. / Williams, C.J. / Adams, P.D. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ahw.cif.gz | 476.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ahw.ent.gz | 327.1 KB | Display | PDB format |
PDBx/mmJSON format | 8ahw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/8ahw ftp://data.pdbj.org/pub/pdb/validation_reports/ah/8ahw | HTTPS FTP |
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-Related structure data
Related structure data | 8b8hC 6sczS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 41278.008 Da / Num. of mol.: 2 / Mutation: D322'N Source method: isolated from a genetically manipulated source Details: LLP is PLP (pyridoxal 5'-phosphate) bound as a cofactor to LYS 44 epsilon amino group (-NH2) via an aldimine linkage or Schiff base Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: ATCC 25618 / H37Rv / Gene: alr, Rv3423c, MTCY78.06 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P9WQA9, alanine racemase #2: Chemical | ChemComp-GOL / | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.4 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 100 mM sodium MES buffer pH 6.2, 150 mM CaCl, 9% (v/v) PEG Smear Broad, 2% (v/v) Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 17, 2018 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→47.35 Å / Num. obs: 109449 / % possible obs: 100 % / Redundancy: 12.3 % / Biso Wilson estimate: 30.03 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.075 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 1.58→1.63 Å / Rmerge(I) obs: 2.54 / Num. unique obs: 10809 / CC1/2: 0.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6SCZ Resolution: 1.58→47.35 Å / SU ML: 0.2313 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5981 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→47.35 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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