+Open data
-Basic information
Entry | Database: PDB / ID: 6h6s | ||||||
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Title | Sad phasing on nickel-substituted human carbonic anhydrase II | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | HYDROLASE / CAII / nickel / SAD | ||||||
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 / arylesterase activity / regulation of chloride transport / 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 / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / 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 / SAD / Resolution: 1.45 Å | ||||||
Authors | Calderone, V. / Fragai, M. / Silva, J.P. / Luchinat, C. / Ravera, E. / Geraldes, C.F.G.C. / Macedo, A.L. / Cerofolini, L. / Giuntini, S. | ||||||
Citation | Journal: J. Biol. Inorg. Chem. / Year: 2019 Title: Non-crystallographic symmetry in proteins: Jahn-Teller-like and Butterfly-like effects? Authors: Silva, J.M. / Giuntini, S. / Cerofolini, L. / Geraldes, C.F.G.C. / Macedo, A.L. / Ravera, E. / Fragai, M. / Luchinat, C. / Calderone, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6h6s.cif.gz | 240.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h6s.ent.gz | 201.1 KB | Display | PDB format |
PDBx/mmJSON format | 6h6s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/6h6s ftp://data.pdbj.org/pub/pdb/validation_reports/h6/6h6s | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 29157.863 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase #2: Chemical | ChemComp-NI / #3: Water | ChemComp-HOH / | |
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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: 2.06 Å3/Da / Density % sol: 40.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 100 mM HEPES, 2.9 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.48306 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.48306 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→45.34 Å / Num. obs: 154486 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.45→1.54 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.29 / Num. unique obs: 22243 / CC1/2: 0.93 / % possible all: 83.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.45→45.34 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.602 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.076 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.416 Å2
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Refinement step | Cycle: 1 / Resolution: 1.45→45.34 Å
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Refine LS restraints |
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