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Yorodumi- PDB-3noo: Crystal Structure of C101A Isocyanide Hydratase from Pseudomonas ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3noo | ||||||
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Title | Crystal Structure of C101A Isocyanide Hydratase from Pseudomonas fluorescens | ||||||
Components | ThiJ/PfpI family protein | ||||||
Keywords | LYASE / DJ-1 superfamily / isocyanide hydratase / isonitrile hydratase | ||||||
Function / homology | DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / ACETATE ION / Isonitrile hydratase InhA Function and homology information | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.03 Å | ||||||
Authors | Lakshminarasimhan, M. / Madzelan, P. / Nan, R. / Milkovic, N.M. / Wilson, M.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Evolution of New Enzymatic Function by Structural Modulation of Cysteine Reactivity in Pseudomonas fluorescens Isocyanide Hydratase. Authors: Lakshminarasimhan, M. / Madzelan, P. / Nan, R. / Milkovic, N.M. / 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 | 3noo.cif.gz | 209.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3noo.ent.gz | 168.5 KB | Display | PDB format |
PDBx/mmJSON format | 3noo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/3noo ftp://data.pdbj.org/pub/pdb/validation_reports/no/3noo | HTTPS FTP |
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-Related structure data
Related structure data | 3nonSC 3noqC 3norC 3novC S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 24148.582 Da / Num. of mol.: 2 / Mutation: C101A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: PFL_4109 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4K977, EC: 4.2.1.103 #2: Chemical | ChemComp-EDO / #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 1.92 Å3/Da / Density % sol: 36.03 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: 24-26% PEG 3350, 200-250 mM magnesium chloride, 100 mM Tris-HCl pH=8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2007 / Details: Bent conical Si-mirror (Rh coated) |
Radiation | Monochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.03→20 Å / Num. all: 178460 / Num. obs: 178460 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 1.03→1.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.7 / Num. unique all: 17028 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3NON Resolution: 1.03→20 Å / Num. parameters: 37112 / Num. restraintsaints: 49471 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: BABINET | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 29 / Occupancy sum hydrogen: 3338.66 / Occupancy sum non hydrogen: 3839.1 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.03→20 Å
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Refine LS restraints |
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