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- PDB-3boc: Carbonic anhydrase from marine diatom Thalassiosira weissflogii- ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3boc | ||||||
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Title | Carbonic anhydrase from marine diatom Thalassiosira weissflogii- zinc bound domain 2 (CDCA1-R2) | ||||||
![]() | Cadmium-specific carbonic anhydrase | ||||||
![]() | LYASE / carbonic anhydrase / marine diatom / zinc-bound | ||||||
Function / homology | Cadmium carbonic anhydrase repeat / Cadmium carbonic anhydrase repeat / metal ion binding / Cadmium-specific carbonic anhydrase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Xu, Y. / Feng, L. / Jeffrey, P.D. / Shi, Y. / Morel, F.M.M. | ||||||
![]() | ![]() Title: Structure and metal exchange in the cadmium carbonic anhydrase of marine diatoms. Authors: Xu, Y. / Feng, L. / Jeffrey, P.D. / Shi, Y. / Morel, F.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.9 KB | Display | ![]() |
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PDB format | ![]() | 38.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 418.5 KB | Display | ![]() |
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Full document | ![]() | 419.6 KB | Display | |
Data in XML | ![]() | 10.9 KB | Display | |
Data in CIF | ![]() | 15 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22432.449 Da / Num. of mol.: 1 / Fragment: Domain 2, CDCA1-R2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | RELATIVE TO THE ORIGINAL COORDINATES THE ZINC AND WATER MOLECULE NUMBERING HAS BEEN OFFSET BY 1000, ...RELATIVE TO THE ORIGINAL COORDINATE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.03 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M sodium citrate, 20% (w/v) PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 4, 2006 |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→100 Å / Num. all: 17726 / Num. obs: 17726 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 23.4 Å2 / Rsym value: 0.054 |
Reflection shell | Resolution: 1.8→1.86 Å / Rsym value: 0.284 / % possible all: 88 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.9538 Å2 / ksol: 0.335251 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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