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Yorodumi- PDB-5g0b: An unusual natural product primary sulfonamide: synthesis, carbon... -
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-Basic information
Entry | Database: PDB / ID: 5g0b | ||||||
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Title | An unusual natural product primary sulfonamide: synthesis, carbonic anhydrase inhibition and protein x-ray structure of Psammaplin C | ||||||
Components | CARBONIC ANHYDRASE 2 | ||||||
Keywords | LYASE / PROTEIN ENGINEERING / NATURAL PRODUCT INHIBITOR / CARBONIC ANHYDRASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Mujumdar, P. / Supuran, C.T. / Peat, T.S. / Poulsen, S.A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: An Unusual Natural Product Primary Sulfonamide: Synthesis, Carbonic Anhydrase Inhibition and Protein X-Ray Structures of Psammaplin C. Authors: Mujumdar, P. / Teruya, K. / Tonissen, K.F. / Vullo, D. / Supuran, C.T. / Peat, T.S. / Poulsen, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g0b.cif.gz | 129.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g0b.ent.gz | 100.9 KB | Display | PDB format |
PDBx/mmJSON format | 5g0b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/5g0b ftp://data.pdbj.org/pub/pdb/validation_reports/g0/5g0b | HTTPS FTP |
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-Related structure data
Related structure data | 5a6hSC 5g01C 5g03C 5g0cC C: citing same article (ref.) 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: 29226.859 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, UNP RESIDUES 1-260 / Mutation: YES Source method: isolated from a genetically manipulated source Details: CAII BACKBONE WITH CATALYTIC SITE MUTATIONS TO MAKE IT LOOK LIKE CAXII Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P00918, carbonic anhydrase |
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-Non-polymers , 5 types, 248 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | CAII BACKBONE SEQUENCE WITH MUTATIONS IN THE CATALYTIC SITE TO MAKE A CAXII MIMIC, WITH THE ...CAII BACKBONE SEQUENCE WITH MUTATIONS IN THE CATALYTIC SITE TO MAKE A CAXII MIMIC, WITH THE FOLLOWING CHANGES A65S, N67Q, E69T, I91L, F131V, G132D, V135L, K170E, L204A, C206G |
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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: 2.09 Å3/Da / Density % sol: 41.2 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 8.5 Details: SITTING DROPS WITH 150 NL PROTEIN AT 5.5 MG/ML WITH 120 NL RESERVOIR AND 30 NL SEEDS. THE RESERVOIR HAD 2.6 TO 2.8 M AMMONIUM SULFATE WITH 100 MM TRIS PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→41.3 Å / Num. obs: 34094 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.6 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5A6H Resolution: 1.55→69.93 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.388 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. THE CHLORIDE ION IS IN SOME POSITIVE DENSITY WHICH IS OTHERWISE UNMODELLED.
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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: 16.503 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→69.93 Å
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Refine LS restraints |
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