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Yorodumi- PDB-1pby: Structure of the Phenylhydrazine Adduct of the Quinohemoprotein A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pby | |||||||||
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Title | Structure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase from Paracoccus denitrificans at 1.7 A Resolution | |||||||||
Components | (quinohemoprotein amine dehydrogenase ...) x 3 | |||||||||
Keywords | OXIDOREDUCTASE / QUINOHEMOPROTEIN / AMINE DEHYDROGENASE | |||||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-NH2 group of donors; With a cytochrome as acceptor / oxidoreductase activity, acting on the CH-NH2 group of donors / periplasmic space / electron transfer activity / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Paracoccus denitrificans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / refined directly / Resolution: 1.7 Å | |||||||||
Authors | Datta, S. / Ikeda, T. / Kano, K. / Mathews, F.S. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Structure of the phenylhydrazine adduct of the quinohemoprotein amine dehydrogenase from Paracoccus denitrificans at 1.7 A resolution. Authors: Datta, S. / Ikeda, T. / Kano, K. / Mathews, F.S. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: Structure of a quinohemoprotein amine dehydrogenase with an uncommon redox cofactor and highly unusual crosslinking | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pby.cif.gz | 223.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pby.ent.gz | 172.1 KB | Display | PDB format |
PDBx/mmJSON format | 1pby.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pby_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1pby_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1pby_validation.xml.gz | 50.4 KB | Display | |
Data in CIF | 1pby_validation.cif.gz | 77.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/1pby ftp://data.pdbj.org/pub/pdb/validation_reports/pb/1pby | HTTPS FTP |
-Related structure data
Related structure data | 1jjuS 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
-Quinohemoprotein amine dehydrogenase ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 52711.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Production host: Paracoccus denitrificans (bacteria) / Strain (production host): IFO12442 / References: UniProt: Q8VUT0, EC: 1.4.99.3 |
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#2: Protein | Mass: 37021.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Production host: Paracoccus denitrificans (bacteria) / References: GenBank: 17402571, UniProt: Q8VUS7*PLUS |
#3: Protein | Mass: 8843.791 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Production host: Paracoccus denitrificans (bacteria) / References: GenBank: 17402570, UniProt: Q8VUS8*PLUS |
-Non-polymers , 3 types, 1301 molecules
#4: Chemical | #5: Chemical | ChemComp-TBU / #6: 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: 2.66 Å3/Da / Density % sol: 53.74 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: PEG 4000, sodium citrate, t-butyl alcohol, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||
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: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 16, 2001 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→36.24 Å / Num. all: 117161 / Num. obs: 110131 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Redundancy: 6.76 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 27.7 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.3 / Num. unique all: 8700 / % possible all: 75.4 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 30 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS Highest resolution: 1.7 Å / % possible obs: 75.4 % / Mean I/σ(I) obs: 2.4 |
-Processing
Software |
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Refinement | Method to determine structure: refined directly Starting model: PDB ENTRY 1JJU Resolution: 1.7→36.42 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 22.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→36.42 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: 6
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Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 10 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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