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Yorodumi- PDB-8vpw: Pseudomonas fluorescens G150T isocyanide hydratase at 298 K XFEL ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vpw | |||||||||
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Title | Pseudomonas fluorescens G150T isocyanide hydratase at 298 K XFEL data, free enzyme | |||||||||
Components | Isonitrile hydratase InhA | |||||||||
Keywords | LYASE / isocyanide / isonitrile / X-ray free electron laser / serial crystallography | |||||||||
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 / FREE ELECTRON LASER / FOURIER SYNTHESIS / Resolution: 1.3 Å | |||||||||
Authors | Wilson, M.A. / Smith, N. / Dasgupta, M. / Dolamore, C. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Sci Adv / Year: 2024 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 3rd, 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 3rd, F.R. / Mittan-Moreau, D.W. / 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vpw.cif.gz | 184.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vpw.ent.gz | 129.3 KB | Display | PDB format |
PDBx/mmJSON format | 8vpw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vpw_validation.pdf.gz | 418.6 KB | Display | wwPDB validaton report |
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Full document | 8vpw_full_validation.pdf.gz | 418.7 KB | Display | |
Data in XML | 8vpw_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 8vpw_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/8vpw ftp://data.pdbj.org/pub/pdb/validation_reports/vp/8vpw | HTTPS FTP |
-Related structure data
Related structure data | 8vq1C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 24224.699 Da / Num. of mol.: 1 / Mutation: G150T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: NRRL B-23932 / PF-5 / Gene: inhA, PFL_4109 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4K977 |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.34 % / Description: plate-like crystals |
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Crystal grow | Temperature: 298 K / Method: batch mode / pH: 8.8 Details: 15.5% PEG 3350, 125 MM MGCL2, AND 62 MM TRIS-HCL PH 8.8 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.033 Å |
Detector | Type: RAYONIX MX340-HS / Detector: CCD / Date: Apr 10, 2021 / Frequency: 30 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→22 Å / Num. obs: 52803 / % possible obs: 99.97 % / Redundancy: 54.11 % / Biso Wilson estimate: 13.28 Å2 / CC1/2: 0.986 / R split: 0.133 / Net I/σ(I): 5 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 16.43 % / Mean I/σ(I) obs: 1.32 / Num. unique obs: 2562 / CC1/2: 0.428 / R split: 0.625 / % possible all: 100 |
Serial crystallography measurement | Focal spot size: 9 µm2 / Pulse duration: 40 fsec. / Pulse photon energy: 12 keV / XFEL pulse repetition rate: 30 Hz |
Serial crystallography sample delivery | Description: coMESH / Method: injection |
Serial crystallography sample delivery injection | Carrier solvent: crystallization buffer / Flow rate: 6 µL/min / Injector diameter: 100 µm / Injector temperature: 298 K / Power by: HPLC |
Serial crystallography data reduction | Crystal hits: 19135 / Lattices indexed: 20796 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.3→22 Å / SU ML: 0.128 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.9598 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: 18.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→22 Å
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Refine LS restraints |
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LS refinement shell |
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