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Open data
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Basic information
Entry | Database: PDB / ID: 2zhv | ||||||
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Title | Crystal structure of BACE1 at pH 7.0 | ||||||
![]() | Beta-secretase 1![]() | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shimizu, H. / Nukina, N. | ||||||
![]() | ![]() Title: Crystal structure of an active form of BACE1, an enzyme responsible for amyloid beta protein production Authors: Shimizu, H. / Tosaki, A. / Kaneko, K. / Hisano, T. / Sakurai, T. / Nukina, N. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93.1 KB | Display | ![]() |
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PDB format | ![]() | 69.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2zhrC ![]() 2zhsC ![]() 2zhtC ![]() 2zhuC ![]() 1w50S C: citing same article ( 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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Unit cell |
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Components
#1: Protein | ![]() Mass: 45900.500 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP residues 45-454 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.19 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 22% PEG 5000 MME, 0.2M Sodium Acetate pH 6.5, 0.2M Ammonium Iodide, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 28, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.85→100 Å / Num. obs: 44019 / % possible obs: 95.7 % / Redundancy: 5 % / Rsym value: 0.048 / Net I/σ(I): 40.1 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 3739 / Rsym value: 0.341 / % possible all: 83.3 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1W50 Resolution: 1.85→49.01 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3013944.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.0145 Å2 / ksol: 0.361145 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 35.2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→49.01 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 1.85 Å / Total num. of bins used: 6 /
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Xplor file |
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