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- PDB-3ef4: Crystal structure of native pseudoazurin from Hyphomicrobium deni... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ef4 | ||||||
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Title | Crystal structure of native pseudoazurin from Hyphomicrobium denitrificans | ||||||
![]() | Blue copper protein | ||||||
![]() | ELECTRON TRANSPORT / copper / electron transfer / blue copper protein | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hira, D. / Nojiri, M. / Suzuki, S. | ||||||
![]() | ![]() Title: Atomic resolution structure of pseudoazurin from the methylotrophic denitrifying bacterium Hyphomicrobium denitrificans: structural insights into its spectroscopic properties Authors: Hira, D. / Nojiri, M. / Suzuki, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 181.6 KB | Display | ![]() |
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PDB format | ![]() | 144.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.5 KB | Display | ![]() |
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Full document | ![]() | 467.5 KB | Display | |
Data in XML | ![]() | 23.7 KB | Display | |
Data in CIF | ![]() | 34.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1adwS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 13590.666 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Chemical | #3: Chemical | ChemComp-PO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.75 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 3.2M Ammonium Phosphate, 0.05M Potassium Phosphate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Jun 13, 2006 |
Radiation | Monochromator: double 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: 1.18→49.2 Å / Num. all: 132934 / Num. obs: 132934 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 43.59 |
Reflection shell | Resolution: 1.18→1.22 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.78 / % possible all: 85.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1adw Resolution: 1.18→44.95 Å / Num. parameters: 32026 / Num. restraintsaints: 45026 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Num. disordered residues: 30 / Occupancy sum hydrogen: 2724 / Occupancy sum non hydrogen: 3402 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.18→44.95 Å
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Refine LS restraints |
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