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Yorodumi- PDB-5bru: Catalytic Improvement of an Artificial Metalloenzyme by Computati... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bru | ||||||
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Title | Catalytic Improvement of an Artificial Metalloenzyme by Computational Design | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | OXIDOREDUCTASE / artificial metalloenzyme | ||||||
Function / homology | Function and homology information positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / morphogenesis of an epithelium / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / one-carbon metabolic process / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å | ||||||
Authors | Heinisch, T. / Pellizzoni, M. / Duerrenberger, M. / Tinberg, C.E. / Koehler, V. / Klehr, J. / Haeussinger, D. / Baker, D. / Ward, T.R. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2015 Title: Improving the Catalytic Performance of an Artificial Metalloenzyme by Computational Design. Authors: Heinisch, T. / Pellizzoni, M. / Durrenberger, M. / Tinberg, C.E. / Kohler, V. / Klehr, J. / Haussinger, D. / Baker, D. / Ward, T.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bru.cif.gz | 126.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bru.ent.gz | 98.1 KB | Display | PDB format |
PDBx/mmJSON format | 5bru.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5bru_validation.pdf.gz | 777 KB | Display | wwPDB validaton report |
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Full document | 5bru_full_validation.pdf.gz | 778.7 KB | Display | |
Data in XML | 5bru_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 5bru_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/5bru ftp://data.pdbj.org/pub/pdb/validation_reports/br/5bru | HTTPS FTP |
-Related structure data
Related structure data | 5brvC 5brwC 3zp9S 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: 29292.125 Da / Num. of mol.: 1 / Mutation: L140M, L197M, C205S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pACA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00918, carbonic anhydrase | ||
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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | ChemComp-8TH / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.9 / Details: 2.6 M ammonium sulfate, 50 mM Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.3051 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2015 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.3051 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.6→70.11 Å / Num. obs: 29218 / % possible obs: 90.3 % / Redundancy: 4.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.048 / Net I/σ(I): 11.6 / Num. measured all: 137882 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZP9 Resolution: 1.6→70.11 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.661 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.147 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→70.11 Å
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