+Open data
-Basic information
Entry | Database: PDB / ID: 3m1k | ||||||
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Title | Carbonic Anhydrase in complex with fragment | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / 10 Stranded Twisted Beta-Sheets / Disease mutation / Metal-binding | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.35 Å | ||||||
Authors | Schulze Wischeler, J. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: Chemmedchem / Year: 2010 Title: Bidentate Zinc chelators for alpha-carbonic anhydrases that produce a trigonal bipyramidal coordination geometry. Authors: Schulze Wischeler, J. / Innocenti, A. / Vullo, D. / Agrawal, A. / Cohen, S.M. / Heine, A. / Supuran, C.T. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3m1k.cif.gz | 128.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m1k.ent.gz | 98.2 KB | Display | PDB format |
PDBx/mmJSON format | 3m1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m1/3m1k ftp://data.pdbj.org/pub/pdb/validation_reports/m1/3m1k | HTTPS FTP |
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-Related structure data
Related structure data | 2oq5S 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
#1: Protein | Mass: 29806.588 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): BL21 Codon Plus / References: UniProt: P00918, carbonic anhydrase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-BEW / |
#4: Chemical | ChemComp-BE7 / ( |
#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: 2.17 Å3/Da / Density % sol: 40.29 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 2.5 M ammonium sulfate 50 mM Tris 0.1 mM p-Chloromercuribenzoicacid 1 mM Fragment, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 110 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: May 31, 2008 / Details: silicon |
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: 1.35→25 Å / Num. all: 50925 / Num. obs: 50925 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rsym value: 0.051 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 2347 / Rsym value: 0.254 / % possible all: 88.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2OQ5 Resolution: 1.35→10 Å / Num. parameters: 20867 / Num. restraintsaints: 26352 / Cross valid method: FREE R / σ(F): 4 / 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: 11 / Occupancy sum hydrogen: 1976 / Occupancy sum non hydrogen: 2280.6 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→10 Å
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Refine LS restraints |
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