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Yorodumi- PDB-3boj: Carbonic anhydrase from marine diatom Thalassiosira weissflogii- ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3boj | ||||||
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Title | Carbonic anhydrase from marine diatom Thalassiosira weissflogii- cadmium bound domain 1 without bound metal (CDCA1-R1) | ||||||
Components | Cadmium-specific carbonic anhydrase | ||||||
Keywords | LYASE / carbonic anhydrase / marine diatom / apo form | ||||||
Function / homology | Cadmium carbonic anhydrase repeat / Cadmium carbonic anhydrase repeat / metal ion binding / ACETATE ION / Cadmium-specific carbonic anhydrase Function and homology information | ||||||
Biological species | Thalassiosira weissflogii (Diatom) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Xu, Y. / Feng, L. / Jeffrey, P.D. / Shi, Y. / Morel, F.M.M. | ||||||
Citation | Journal: Nature / Year: 2008 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3boj.cif.gz | 58.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3boj.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 3boj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3boj_validation.pdf.gz | 441.3 KB | Display | wwPDB validaton report |
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Full document | 3boj_full_validation.pdf.gz | 442.5 KB | Display | |
Data in XML | 3boj_validation.xml.gz | 12 KB | Display | |
Data in CIF | 3boj_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/3boj ftp://data.pdbj.org/pub/pdb/validation_reports/bo/3boj | HTTPS FTP |
-Related structure data
Related structure data | 3bobC 3bocC 3boeC 3bohSC 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
#1: Protein | Mass: 23069.201 Da / Num. of mol.: 1 / Fragment: Domain 1, CDCA1-R1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thalassiosira weissflogii (Diatom) / Gene: cdca1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q50EL4, carbonic anhydrase |
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#2: Chemical | ChemComp-ACT / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | RELATIVE TO THE ORIGINAL COORDINATES THE ACETATE AND WATER MOLECULE NUMBERING HAS BEEN OFFSET BY ...RELATIVE TO THE ORIGINAL COORDINATE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.5 M NaH2PO4, 1.4 M K2HPO4, 0.1M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 19, 2007 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. all: 39051 / Num. obs: 39051 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 14.3 Å2 / Rsym value: 0.075 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 2.5 % / Rsym value: 0.363 / % possible all: 90.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CDCA1-R1 cadmium bound form, PDB entry 3BOH Resolution: 1.45→33.04 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1179673.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.9868 Å2 / ksol: 0.385679 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.45→33.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.54 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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