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Open data
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Basic information
Entry | Database: PDB / ID: 3zki | ||||||
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Title | BACE2 MUTANT STRUCTURE WITH LIGAND | ||||||
![]() | BETA-SECRETASE 2 | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() memapsin 1 / negative regulation of amyloid precursor protein biosynthetic process / melanosome membrane / melanosome organization / peptide hormone processing / membrane protein ectodomain proteolysis / amyloid-beta metabolic process / trans-Golgi network / protein processing / glucose homeostasis ...memapsin 1 / negative regulation of amyloid precursor protein biosynthetic process / melanosome membrane / melanosome organization / peptide hormone processing / membrane protein ectodomain proteolysis / amyloid-beta metabolic process / trans-Golgi network / protein processing / glucose homeostasis / aspartic-type endopeptidase activity / endosome / Golgi apparatus / endoplasmic reticulum / proteolysis / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Banner, D.W. / Kuglstatter, A. / Benz, J. / Stihle, M. / Ruf, A. | ||||||
![]() | ![]() Title: Mapping the Conformational Space Accessible to Bace2 Using Surface Mutants and Co-Crystals with Fab-Fragments, Fynomers, and Xaperones Authors: Banner, D.W. / Gsell, B. / Benz, J. / Bertschinger, J. / Burger, D. / Brack, S. / Cuppuleri, S. / Debulpaep, M. / Gast, A. / Grabulovski, D. / Hennig, M. / Hilpert, H. / Huber, W. / ...Authors: Banner, D.W. / Gsell, B. / Benz, J. / Bertschinger, J. / Burger, D. / Brack, S. / Cuppuleri, S. / Debulpaep, M. / Gast, A. / Grabulovski, D. / Hennig, M. / Hilpert, H. / Huber, W. / Kuglstatter, A. / Kusznir, E. / Laeremans, T. / Matile, H. / Miscenic, C. / Rufer, A. / Schlatter, D. / Steyeart, J. / Stihle, M. / Thoma, R. / Weber, M. / Ruf, A. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160.2 KB | Display | ![]() |
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PDB format | ![]() | 125.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 885.7 KB | Display | ![]() |
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Full document | ![]() | 892.9 KB | Display | |
Data in XML | ![]() | 30 KB | Display | |
Data in CIF | ![]() | 42.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zkgSC ![]() 3zkmC ![]() 3zknC ![]() 3zkqC ![]() 3zksC ![]() 3zkxC ![]() 3zl7C ![]() 3zovC ![]() 4belC ![]() 4bfbC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 42047.355 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR, RESIDUES 75-460 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE PDB FILE IS NUMBERED AFTER PDB-ENTRY 2EWY WHICH HAS NUMBERS 62 LESS THAN THE DATA BANK SEQUENCE. ...THE PDB FILE IS NUMBERED AFTER PDB-ENTRY 2EWY WHICH HAS NUMBERS 62 LESS THAN THE DATA BANK SEQUENCE. THE MUTATION HERE IS E269A IN THE PDB FILE AND E331A IN THE DATA BANK SEQUENCE. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.4 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 0.1M TRIS PH8.0, 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 14, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→49.1 Å / Num. obs: 31592 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 2.54 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 2.53 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ZKG Resolution: 2.4→49.06 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.913 / SU B: 8.838 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.482 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. MOLECULES A AND B ARE RELATED BY A LOCAL PSEUDO-DYAD AXIS. NCS CONSTRAINTS WERE NOT USED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.468 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→49.06 Å
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Refine LS restraints |
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