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Yorodumi- PDB-7lav: Pseudomonas fluorescens G150T isocyanide hydratase (G150T-1) at 2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lav | |||||||||
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Title | Pseudomonas fluorescens G150T isocyanide hydratase (G150T-1) at 274K, Refmac5-refined | |||||||||
Components | Isonitrile hydratase InhA | |||||||||
Keywords | LYASE / DJ-1/PfpI superfamily | |||||||||
Function / homology | DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase-like / Isonitrile hydratase InhA Function and homology information | |||||||||
Biological species | Pseudomonas fluorescens (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.149 Å | |||||||||
Authors | Su, Z. / Dasgupta, M. / Poitevin, F. / Mathews, I.I. / van den Bedem, H. / Wall, M.E. / Yoon, C.H. / Wilson, M.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Struct Dyn. / Year: 2021 Title: Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters. Authors: Su, Z. / Dasgupta, M. / Poitevin, F. / Mathews, I.I. / van den Bedem, H. / Wall, M.E. / Yoon, C.H. / 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 | 7lav.cif.gz | 110 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lav.ent.gz | 81.5 KB | Display | PDB format |
PDBx/mmJSON format | 7lav.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/7lav ftp://data.pdbj.org/pub/pdb/validation_reports/la/7lav | HTTPS FTP |
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-Related structure data
Related structure data | 7l9qC 7l9sC 7l9wC 7l9zC 7la0C 7la3C 7laxC 7lb9C 7lbhC 7lbiC 7lcxC 7ld6C 7ld7C 7ldbC 7ldiC 7ldmC 7ldoC 6ni4S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-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 (strain ATCC BAA-477 / NRRL B-23932 / Pf-5) (bacteria) Strain: ATCC BAA-477 / NRRL B-23932 / Pf-5 / Gene: inhA, PFL_4109 / Plasmid: pet15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q4K977 |
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#2: Water | ChemComp-HOH / |
-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: 45.41 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 25% PEG 3350, 200 MM MAGNESIUM CHLORIDE, 100MM TRIS-HCL, PH 8.6, 2 MM dithiothreitol |
-Data collection
Diffraction | Mean temperature: 274 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: Nov 28, 2018 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: 1.149→39.5 Å / Num. obs: 74206 / % possible obs: 97.4 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rrim(I) all: 0.052 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.149→1.17 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3528 / CC1/2: 0.366 / Rrim(I) all: 1.72 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6NI4 Resolution: 1.149→39.5 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.986 / SU B: 1.237 / SU ML: 0.024 / Cross valid method: FREE R-VALUE / ESU R: 0.03 / ESU R Free: 0.029 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.333 Å2
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Refinement step | Cycle: LAST / Resolution: 1.149→39.5 Å
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Refine LS restraints |
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LS refinement shell |
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