+Open data
-Basic information
Entry | Database: PDB / ID: 8tsx | ||||||
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Title | Pseudomonas fluorescens G150T isocyanide hydratase at 100 K | ||||||
Components | Isonitrile hydratase InhA | ||||||
Keywords | LYASE / isocyanide / isonitrile | ||||||
Function / homology | DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase-like / regulation of DNA-templated transcription / Isonitrile hydratase InhA Function and homology information | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å | ||||||
Authors | Wilson, M.A. / Smith, N. / Dasgupta, M. / Dolamore, C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biorxiv / Year: 2023 Title: Changes in an Enzyme Ensemble During Catalysis Observed by High Resolution XFEL Crystallography. Authors: Smith, N. / Dasgupta, M. / Wych, D.C. / Dolamore, C. / Sierra, R.G. / Lisova, S. / Marchany-Rivera, D. / Cohen, A.E. / Boutet, S. / Hunter, M.S. / Kupitz, C. / Poitevin, F. / Moss, F.R. / ...Authors: Smith, N. / Dasgupta, M. / Wych, D.C. / Dolamore, C. / Sierra, R.G. / Lisova, S. / Marchany-Rivera, D. / Cohen, A.E. / Boutet, S. / Hunter, M.S. / Kupitz, C. / Poitevin, F. / Moss, F.R. / Brewster, A.S. / Sauter, N.K. / Young, I.D. / Wolff, A.M. / Tiwari, V.K. / Kumar, N. / Berkowitz, D.B. / Hadt, R.G. / Thompson, M.C. / Follmer, A.H. / Wall, M.E. / Wilson, M.A. #1: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tsx.cif.gz | 384 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tsx.ent.gz | 265.4 KB | Display | PDB format |
PDBx/mmJSON format | 8tsx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tsx_validation.pdf.gz | 434.7 KB | Display | wwPDB validaton report |
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Full document | 8tsx_full_validation.pdf.gz | 436.2 KB | Display | |
Data in XML | 8tsx_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 8tsx_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ts/8tsx ftp://data.pdbj.org/pub/pdb/validation_reports/ts/8tsx | HTTPS FTP |
-Related structure data
Related structure data | 8tsuC 8tsyC 8tszC 8tt0C 8tt1C 8tt2C 8tt4C 8tt5C C: citing same article (ref.) |
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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: 24224.699 Da / Num. of mol.: 2 / Mutation: G150T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: inhA, PFL_4109 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4K977 #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.16 Å3/Da / Density % sol: 43.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.8 Details: 23% PEG 3350, 200 mM MgCl2, 100 mM Tris-HCl pH=8.8, and 2 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.775 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2022 Details: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.775 Å / Relative weight: 1 |
Reflection | Resolution: 1→38.87 Å / Num. obs: 218349 / % possible obs: 98.1 % / Redundancy: 4.7 % / Biso Wilson estimate: 11.72 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.063 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1→1.02 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 10505 / CC1/2: 0.262 / Rrim(I) all: 2.85 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1→38.87 Å / SU ML: 0.1101 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.055 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→38.87 Å
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Refine LS restraints |
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LS refinement shell |
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