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Yorodumi- PDB-4q49: Room temperature neutron crystal structure of apo human carbonic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q49 | ||||||
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Title | Room temperature neutron crystal structure of apo human carbonic anhydrase at pH 7.5 | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / mixed alpha beta / proton transfer / cytosolic | ||||||
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 / 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 / zinc ion binding / extracellular exosome / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Fisher, S.Z. / McKenna, R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Joint neutron crystallographic and NMR solution studies of Tyr residue ionization and hydrogen bonding: Implications for enzyme-mediated proton transfer. Authors: Michalczyk, R. / Unkefer, C.J. / Bacik, J.P. / Schrader, T.E. / Ostermann, A. / Kovalevsky, A.Y. / McKenna, R. / Fisher, S.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q49.cif.gz | 122.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q49.ent.gz | 95.8 KB | Display | PDB format |
PDBx/mmJSON format | 4q49.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4q49_validation.pdf.gz | 166.4 KB | Display | wwPDB validaton report |
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Full document | 4q49_full_validation.pdf.gz | 166.3 KB | Display | |
Data in XML | 4q49_validation.xml.gz | 681 B | Display | |
Data in CIF | 4q49_validation.cif.gz | 3.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/4q49 ftp://data.pdbj.org/pub/pdb/validation_reports/q4/4q49 | HTTPS FTP |
-Related structure data
Related structure data | 4y0jC 3gz0S 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: 29289.062 Da / Num. of mol.: 1 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 |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-DOD / |
-Experimental details
-Experiment
Experiment | Method: NEUTRON DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.20 M sodium citrate 100 mM Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: NUCLEAR REACTOR / Site: FRM II / Beamline: BIODIFF / Wavelength: 2.66 Å |
Detector | Type: MAATEL BIODIFF / Detector: IMAGE PLATE / Date: Apr 1, 2013 |
Radiation | Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron |
Radiation wavelength | Wavelength: 2.66 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 23230 / Num. obs: 20884 / % possible obs: 89.9 % / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.8→1.85 Å / % possible all: 76.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3gz0 Resolution: 1.8→19.998 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 19.27 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→19.998 Å
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Refine LS restraints |
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LS refinement shell |
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