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Yorodumi- PDB-4ifk: Arginines 51 and 239* from a Neighboring Subunit are Essential fo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ifk | ||||||
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Title | Arginines 51 and 239* from a Neighboring Subunit are Essential for Catalysis in a Zinc-dependent Decarboxylase | ||||||
Components | (2-amino-3-carboxymuconate 6-semialdehyde decarboxylase) x 2 | ||||||
Keywords | LYASE / TIM-BARREL / Decarboxylation / Metal-binding | ||||||
Function / homology | Function and homology information organic substance metabolic process / carboxy-lyase activity / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.012 Å | ||||||
Authors | Huo, L. / Davis, I. / Chen, L. / Liu, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: The power of two: arginine 51 and arginine 239* from a neighboring subunit are essential for catalysis in alpha-amino-beta-carboxymuconate-epsilon-semialdehyde decarboxylase. Authors: Huo, L. / Davis, I. / Chen, L. / Liu, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ifk.cif.gz | 147 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ifk.ent.gz | 113.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ifk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/4ifk ftp://data.pdbj.org/pub/pdb/validation_reports/if/4ifk | HTTPS FTP |
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-Related structure data
Related structure data | 4ifoC 4ifrC 4ig2C 2hbvS 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: 36737.977 Da / Num. of mol.: 1 / Mutation: R239A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: KU-7 / Gene: nbaD / Plasmid: PET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83V25 | ||
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#2: Protein | Mass: 36737.977 Da / Num. of mol.: 1 / Mutation: R51A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: KU-7 / Gene: nbaD / Plasmid: PET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83V25 | ||
#3: Chemical | ChemComp-MG / | ||
#4: Chemical | #5: 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: 2.26 Å3/Da / Density % sol: 45.68 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.75 Details: 0.1 M Tris pH 8.75, 0.2 M MgCl2, 17% PEG5000, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.8 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 14, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→35 Å / Num. all: 43915 / Num. obs: 42861 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.107 / Χ2: 2.407 / Net I/σ(I): 11.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2HBV Resolution: 2.012→22.919 Å / Occupancy max: 1 / Occupancy min: 0.08 / FOM work R set: 0.7995 / SU ML: 0.22 / σ(F): 1.34 / Phase error: 26.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.756 Å2 / ksol: 0.334 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.96 Å2 / Biso mean: 39.6565 Å2 / Biso min: 14.76 Å2
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Refinement step | Cycle: LAST / Resolution: 2.012→22.919 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15
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