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Yorodumi- PDB-5a25: Rational engineering of a mesophilic carbonic anhydrase to an ext... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a25 | ||||||
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Title | Rational engineering of a mesophilic carbonic anhydrase to an extreme halotolerant biocatalyst | ||||||
Components | CARBONIC ANHYDRASE 2 | ||||||
Keywords | LYASE / PROTEIN ENGINEERING / BIOCATALYSIS | ||||||
Function / homology | Function and homology information positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / cyanamide hydratase / cyanamide hydratase activity / angiotensin-activated signaling pathway / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / one-carbon metabolic process ...positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / cyanamide hydratase / cyanamide hydratase activity / angiotensin-activated signaling pathway / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / one-carbon metabolic process / apical part of cell / zinc ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | BOS TAURUS (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Warden, A. / Newman, J. / Peat, T.S. / Seabrook, S. / Williams, M. / Dojchinov, G. / Haritos, V. | ||||||
Citation | Journal: Nat.Commun. / Year: 2015 Title: Rational Engineering of a Mesohalophilic Carbonic Anhydrase to an Extreme Halotolerant Biocatalyst. Authors: Warden, A.C. / Williams, M. / Peat, T.S. / Seabrook, S.A. / Newman, J. / Dojchinov, G. / Haritos, V.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a25.cif.gz | 224.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a25.ent.gz | 180.4 KB | Display | PDB format |
PDBx/mmJSON format | 5a25.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/5a25 ftp://data.pdbj.org/pub/pdb/validation_reports/a2/5a25 | HTTPS FTP |
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-Related structure data
Related structure data | 4cnrC 4cnvC 4cnwC 4cnxC 1v9eS 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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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 5 molecules AB
#1: Protein | Mass: 29151.758 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BOS TAURUS (cattle) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00921, carbonic anhydrase #5: Sugar | |
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-Non-polymers , 4 types, 393 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-NA / #6: Water | ChemComp-HOH / | |
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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: 2.4 Å3/Da / Density % sol: 48.8 % / Description: NONE |
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Crystal grow | pH: 8.2 Details: 150 NL 20 MG/ML PROTEIN PLUS 150 NL RESERVOIR CONSISTING OF 50 MM TRIS PH 8.2, 2.3 M AMMONIUM SULFATE, 0.023 (W/V) N-OCTYL-B-D-GLUCOPYRANOSIDE |
-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: Apr 27, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→19.9 Å / Num. obs: 41643 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.88→1.98 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.4 / % possible all: 68.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1V9E Resolution: 1.9→58.84 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.796 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 17.358 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→58.84 Å
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Refine LS restraints |
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