+Open data
-Basic information
Entry | Database: PDB / ID: 1kol | ||||||
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Title | Crystal structure of formaldehyde dehydrogenase | ||||||
Components | formaldehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / dehydrogenase | ||||||
Function / homology | Function and homology information formaldehyde dismutase / formaldehyde dismutase activity / formaldehyde dehydrogenase / formaldehyde dehydrogenase (NAD+) activity / zinc ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å | ||||||
Authors | Tanaka, N. / Kusakabe, Y. / Ito, K. / Yoshimoto, T. / Nakamura, K.T. | ||||||
Citation | Journal: J.mol.biol. / Year: 2002 Title: Crystal Structure of Formaldehyde Dehydrogenase from Pseudomonas putida: the Structural Origin of the Tightly Bound Cofactor in Nicotinoprotein Dehydrogenases Authors: Tanaka, N. / Kusakabe, Y. / Ito, K. / Yoshimoto, T. / Nakamura, K.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kol.cif.gz | 183 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kol.ent.gz | 143.2 KB | Display | PDB format |
PDBx/mmJSON format | 1kol.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/1kol ftp://data.pdbj.org/pub/pdb/validation_reports/ko/1kol | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a tetramer. Two subunits (1/2 tetramer) exist in an asymmetric unit. |
-Components
#1: Protein | Mass: 41987.953 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P46154, formaldehyde dehydrogenase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: 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: 2.41 Å3/Da / Density % sol: 48.88 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Tris, ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30 Å / Num. all: 94085 / Num. obs: 94085 / % possible obs: 97.4 % / Redundancy: 10 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 2.8 / % possible all: 83.9 |
Reflection | *PLUS Lowest resolution: 30 Å |
Reflection shell | *PLUS Lowest resolution: 1.74 Å / % possible obs: 83.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.65→30 Å
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Refinement step | Cycle: LAST / Resolution: 1.65→30 Å
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Refine LS restraints | Type: p_bond_d / Dev ideal: 0.009 | ||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||
Refine LS restraints | *PLUS Type: p_angle_d / Dev ideal: 0.025 |