+Open data
-Basic information
Entry | Database: PDB / ID: 3zl7 | ||||||
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Title | BACE2 FYNOMER COMPLEX | ||||||
Components |
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Keywords | HYDROLASE / ASPARTYL PROTEASE | ||||||
Function / homology | Function and homology information memapsin 1 / negative regulation of amyloid precursor protein biosynthetic process / melanosome organization / melanosome membrane / 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 organization / melanosome membrane / 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) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zl7.cif.gz | 99 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zl7.ent.gz | 74 KB | Display | PDB format |
PDBx/mmJSON format | 3zl7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/3zl7 ftp://data.pdbj.org/pub/pdb/validation_reports/zl/3zl7 | HTTPS FTP |
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-Related structure data
Related structure data | 3zkgC 3zkiC 3zkmC 3zknC 3zkqSC 3zksC 3zkxC 3zovC 4belC 4bfbC 4ag1S 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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Unit cell |
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-Components
#1: Protein | Mass: 42047.355 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, 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 |
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#2: Protein | Mass: 10325.441 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli) |
#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. MODIFIED VERSION OF HUMAN FYN TYROSINE KINASE SH3 DOMAIN |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.1 % Description: DATA COMPROMISED BY DIFFUSE ICE RING AT 3.68A AND APERTURE SCATTER AT 3.24A |
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Crystal grow | pH: 5 / Details: 1.8M NA/K PHOSPHATE, PH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.91→43.77 Å / Num. obs: 10238 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Redundancy: 11.6 % / Biso Wilson estimate: 91.84 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.91→3.01 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 3ZKQ, 4AG1 Resolution: 3.2→43.77 Å / Cor.coef. Fo:Fc: 0.8572 / Cor.coef. Fo:Fc free: 0.7992 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.667 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY. ALL LOWER SYMMETRY SPACE GROUPS WERE TESTED AND REJECTED AS REFINEMENT STATISTICS NOT SIGNIFICANTLY BETTER
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Displacement parameters | Biso mean: 80.23 Å2
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Refine analyze | Luzzati coordinate error obs: 0.86 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→43.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.58 Å / Total num. of bins used: 5
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