[English] 日本語
Yorodumi- PDB-3efi: Carbonic anhydrase activators: Kinetic and X-ray crystallographic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3efi | ||||||
---|---|---|---|---|---|---|---|
Title | Carbonic anhydrase activators: Kinetic and X-ray crystallographic study for the interaction of d- and l-tryptophan with the mammalian isoforms I-XIV | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / carbonic anhydrase / activators / aminoacids / OXO-ACID / Acetylation / Cytoplasm / Disease mutation / Metal-binding / Polymorphism / Zinc | ||||||
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 / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Temperini, C. / Innocenti, A. / Scozzafava, A. / Supuran, C.T. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2008 Title: Carbonic anhydrase activators: kinetic and X-ray crystallographic study for the interaction of D- and L-tryptophan with the mammalian isoforms I-XIV Authors: Temperini, C. / Innocenti, A. / Scozzafava, A. / Supuran, C.T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3efi.cif.gz | 71.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3efi.ent.gz | 51.7 KB | Display | PDB format |
PDBx/mmJSON format | 3efi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/3efi ftp://data.pdbj.org/pub/pdb/validation_reports/ef/3efi | HTTPS FTP |
---|
-Related structure data
Related structure data | 1ca2S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 29289.062 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Chemically synthesized. This sequence occurs naturally in humans(homo sapiens). References: UniProt: P00918, carbonic anhydrase |
---|---|
#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-MBO / |
#4: Chemical | ChemComp-TRP / |
#5: Water | ChemComp-HOH / |
Sequence details | THE NUMBER 126 IS SIMPLY SKIPPED IN THE NUMBERING. THE GAP IS IN THE SEQUENCE NUMBERING OF MODEL ...THE NUMBER 126 IS SIMPLY SKIPPED IN THE NUMBERING. THE GAP IS IN THE SEQUENCE NUMBERING OF MODEL 1CA2, THAT IS THE STARTING MODEL FOR ALL CA2 STRUCTURES |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.61 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 50mM Tris.HCl pH 7.7-7.8, 2mM sodium 4-(hydroxymercury)benzoate, VAPOR DIFFUSION, HANGING DROP, temperature 277K PH range: 7.7-7.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCED ULTRA / Wavelength: 1.5418 Å |
Detector | Type: OXFORD SAPPHIRE CCD / Detector: CCD / Date: Apr 1, 2008 |
Radiation | Monochromator: capillary / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20 Å / Num. obs: 24484 / % possible obs: 99 % / Observed criterion σ(F): 2 / Redundancy: 3.6 % / Rsym value: 0.132 / Net I/σ(I): 15.14 |
Reflection shell | Resolution: 1.75→1.86 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 4080 / Rsym value: 0.303 / % possible all: 99 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CA2 Resolution: 1.75→10.38 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.917 / SU B: 2.708 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 12.767 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→10.38 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
|