+Open data
-Basic information
Entry | Database: PDB / ID: 3zkq | ||||||
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Title | BACE2 XAPERONE COMPLEX | ||||||
Components |
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Keywords | HYDROLASE/IMMUNE SYSTEM / HYDROLASE-IMMUNE SYSTEM COMPLEX / NANOBODY | ||||||
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) LAMA GLAMA (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zkq.cif.gz | 120.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zkq.ent.gz | 90.3 KB | Display | PDB format |
PDBx/mmJSON format | 3zkq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zkq_validation.pdf.gz | 730.9 KB | Display | wwPDB validaton report |
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Full document | 3zkq_full_validation.pdf.gz | 735.5 KB | Display | |
Data in XML | 3zkq_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 3zkq_validation.cif.gz | 35.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/3zkq ftp://data.pdbj.org/pub/pdb/validation_reports/zk/3zkq | HTTPS FTP |
-Related structure data
Related structure data | 3zkgSC 3zkiC 3zkmC 3zknC 3zksC 3zkxC 3zl7C 3zovC 4belC 4bfbC 2xa3S S: Starting model for refinement C: citing same article (ref.) |
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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: 42105.391 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR, RESIDUES 75-460 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: Antibody | Mass: 13152.520 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LAMA GLAMA (llama) / Plasmid: PMESY4 / Production host: ESCHERICHIA COLI (E. coli) |
#3: Chemical | ChemComp-B3P / |
#4: Chemical | ChemComp-CL / |
#5: 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. ANTIBODY RAISED IN LLAMA AGAINST BACE2. V(HH) EXPRESSED IN E. COLI. WITH 6HIS AND EPEA TAG. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.7 % / Description: NONE |
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Crystal grow | Details: 25% PEG1500 |
-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: Oct 5, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→44.5 Å / Num. obs: 83053 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.51→1.61 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.4 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 3ZKG, 2XA3 Resolution: 1.51→44.47 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.894 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS WERE USED BUT NOT OUTPUT. 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: 31.553 Å2
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Refinement step | Cycle: LAST / Resolution: 1.51→44.47 Å
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Refine LS restraints |
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