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Yorodumi- PDB-1ddz: X-RAY STRUCTURE OF A BETA-CARBONIC ANHYDRASE FROM THE RED ALGA, P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ddz | ||||||
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Title | X-RAY STRUCTURE OF A BETA-CARBONIC ANHYDRASE FROM THE RED ALGA, PORPHYRIDIUM PURPUREUM R-1 | ||||||
Components | CARBONIC ANHYDRASE | ||||||
Keywords | LYASE / ALPHA-BETA-ALPHA | ||||||
Function / homology | Function and homology information carbon utilization / carbonic anhydrase / carbonate dehydratase activity / zinc ion binding Similarity search - Function | ||||||
Biological species | Porphyridium purpureum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Mitsuhashi, S. / Mizushima, T. / Yamashita, E. / Miyachi, S. / Tsukihara, T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: X-ray structure of beta-carbonic anhydrase from the red alga, Porphyridium purpureum, reveals a novel catalytic site for CO(2) hydration. Authors: Mitsuhashi, S. / Mizushima, T. / Yamashita, E. / Yamamoto, M. / Kumasaka, T. / Moriyama, H. / Ueki, T. / Miyachi, S. / Tsukihara, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ddz.cif.gz | 206.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ddz.ent.gz | 164.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ddz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ddz_validation.pdf.gz | 375 KB | Display | wwPDB validaton report |
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Full document | 1ddz_full_validation.pdf.gz | 391.9 KB | Display | |
Data in XML | 1ddz_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 1ddz_validation.cif.gz | 34.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/1ddz ftp://data.pdbj.org/pub/pdb/validation_reports/dd/1ddz | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 54993.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Variant: R-1 / Plasmid: PET16B / Production host: Escherichia coli (E. coli) / References: UniProt: Q43060, carbonic anhydrase #2: Chemical | ChemComp-ZN / #3: 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: 2.32 Å3/Da / Density % sol: 46.89 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.75 Details: PEG4000, AMMONIUM SULFATE, SODIUM CACODYLATE, pH 6.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8.5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→60 Å / Num. all: 326527 / Num. obs: 50489 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.227 / % possible all: 99.8 |
Reflection | *PLUS Num. measured all: 326527 |
Reflection shell | *PLUS Num. possible: 27202 / Num. unique obs: 5016 / Mean I/σ(I) obs: 4.5 |
-Processing
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Refinement | Resolution: 2.2→10 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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