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Yorodumi- PDB-1jmz: crystal structure of a quinohemoprotein amine dehydrogenase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jmz | ||||||
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Title | crystal structure of a quinohemoprotein amine dehydrogenase from pseudomonas putida with inhibitor | ||||||
Components | (Amine Dehydrogenase) x 3 | ||||||
Keywords | OXIDOREDUCTASE / Amine Dehydrogenase | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-NH2 group of donors; With a copper protein as acceptor / aliphatic amine dehydrogenase activity / periplasmic space / electron transfer activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Satoh, A. / Miyahara, I. / Hirotsu, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Crystal structure of quinohemoprotein amine dehydrogenase from Pseudomonas putida. Identification of a novel quinone cofactor encaged by multiple thioether cross-bridges. Authors: Satoh, A. / Kim, J.K. / Miyahara, I. / Devreese, B. / Vandenberghe, I. / Hacisalihoglu, A. / Okajima, T. / Kuroda, S. / Adachi, O. / Duine, J.A. / Van Beeumen, J. / Tanizawa, K. / Hirotsu, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jmz.cif.gz | 190.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jmz.ent.gz | 156.8 KB | Display | PDB format |
PDBx/mmJSON format | 1jmz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jmz_validation.pdf.gz | 565.4 KB | Display | wwPDB validaton report |
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Full document | 1jmz_full_validation.pdf.gz | 583 KB | Display | |
Data in XML | 1jmz_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 1jmz_validation.cif.gz | 33.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jm/1jmz ftp://data.pdbj.org/pub/pdb/validation_reports/jm/1jmz | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 3 types, 3 molecules ABG
#1: Protein | Mass: 53986.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria) / References: UniProt: Q8VW85 |
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#2: Protein | Mass: 39284.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria) / References: UniProt: Q8VW82 |
#3: Protein | Mass: 8630.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria) / References: UniProt: P0A182 |
-Non-polymers , 4 types, 300 molecules
#4: Chemical | ChemComp-NI / | ||||
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#5: Chemical | #6: Chemical | ChemComp-PND / | #7: 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: 2.78 Å3/Da / Density % sol: 55.83 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: PEG MME2000, nickel chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 25, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→34 Å / Num. obs: 75744 / % possible obs: 99.9 % / Observed criterion σ(F): 1 |
Reflection shell | Resolution: 2→2.09 Å / % possible all: 99.6 |
Reflection | *PLUS % possible obs: 99.7 % / Rmerge(I) obs: 0.067 |
Reflection shell | *PLUS % possible obs: 99.7 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 2.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.211 / Rfactor Rfree: 0.25 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_bond_d / Dev ideal: 0.009 | |||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.293 / Rfactor obs: 0.279 |