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Yorodumi- PDB-4fu5: Carbonic Anhydrase II in complex with N-[(2Z)-1,3-oxazolidin-2-yl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fu5 | ||||||
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Title | Carbonic Anhydrase II in complex with N-[(2Z)-1,3-oxazolidin-2-ylidene]sulfuric diamide | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE/LYASE INHIBITOR / 10 STRANDED TWISTED BETA-SHEETS / LYASE / LYASE-LYASE INHIBITOR complex | ||||||
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 | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å | ||||||
Authors | Di Pizio, A. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: To be Published Title: HIgh resolution crystal structures of Carbonic Anhzdrase II in complex with nonvel sulfamide binders Authors: Di Pizio, A. / Schulze Wischeler, J. / Haake, M. / Heine, A. / Supuran, C. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fu5.cif.gz | 135 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fu5.ent.gz | 102.2 KB | Display | PDB format |
PDBx/mmJSON format | 4fu5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fu5_validation.pdf.gz | 766.8 KB | Display | wwPDB validaton report |
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Full document | 4fu5_full_validation.pdf.gz | 768.1 KB | Display | |
Data in XML | 4fu5_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 4fu5_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/4fu5 ftp://data.pdbj.org/pub/pdb/validation_reports/fu/4fu5 | HTTPS FTP |
-Related structure data
Related structure data | 4fptS S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#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 / Plasmid: PGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL 21 CODON+ / References: UniProt: P00918, carbonic anhydrase |
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-Non-polymers , 5 types, 338 molecules
#2: Chemical | ChemComp-MBO / | ||
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#3: Chemical | ChemComp-ZN / | ||
#4: Chemical | ChemComp-0VX / | ||
#5: Chemical | #6: 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: 2.09 Å3/Da / Density % sol: 41.21 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 2.75 M AMMONIUMSULFATE, 0.15 mM P-CHLOROMERCURIBENZOIC ACID, 0.1 M TRIS, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2011 |
Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 0.98→30 Å / Num. all: 133357 / Num. obs: 133357 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rsym value: 0.06 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 0.98→1 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2.13 / Num. unique all: 6705 / Rsym value: 0.306 / % possible all: 73 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FPT Resolution: 0.98→30 Å / Num. parameters: 22220 / Num. restraintsaints: 28135 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Refine analyze | Num. disordered residues: 18 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2366.86 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.98→30 Å
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Refine LS restraints |
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