+Open data
-Basic information
Entry | Database: PDB / ID: 3zkg | ||||||
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Title | BACE2 MUTANT APO STRUCTURE | ||||||
Components | BETA-SECRETASE 2 | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information 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 | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Banner, D.W. / Kuglstatter, A. / Benz, J. / Stihle, M. / Ruf, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 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 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zkg.cif.gz | 158.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zkg.ent.gz | 123.5 KB | Display | PDB format |
PDBx/mmJSON format | 3zkg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zkg_validation.pdf.gz | 744.9 KB | Display | wwPDB validaton report |
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Full document | 3zkg_full_validation.pdf.gz | 753.6 KB | Display | |
Data in XML | 3zkg_validation.xml.gz | 30.2 KB | Display | |
Data in CIF | 3zkg_validation.cif.gz | 43 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/3zkg ftp://data.pdbj.org/pub/pdb/validation_reports/zk/3zkg | HTTPS FTP |
-Related structure data
Related structure data | 3zkiC 3zkmC 3zknC 3zkqC 3zksC 3zkxC 3zl7C 3zovC 4belC 4bfbC 2ewyS C: citing same article (ref.) 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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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.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y5Z0, memapsin 1 #2: Chemical | ChemComp-B3P / | #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.5 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 0.1M TRIS PH8, 25% PEG3350, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 20, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→32.8 Å / Num. obs: 61792 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 2.57 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 1.9→1.99 Å / Redundancy: 2.61 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.5 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2EWY Resolution: 1.9→32.82 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.88 / SU B: 4.517 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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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: 27.255 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→32.82 Å
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Refine LS restraints |
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