+Open data
-Basic information
Entry | Database: PDB / ID: 3d0n | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human carbonic anhydrase XIII | ||||||
Components | Carbonic anhydrase 13 | ||||||
Keywords | METAL BINDING PROTEIN / Carbonic anhydrase / Lyase / Metal-binding | ||||||
Function / homology | Function and homology information Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / myelin sheath / intracellular membrane-bounded organelle / zinc ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Di Fiore, A. / De Simone, G. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Crystal structure of human carbonic anhydrase XIII and its complex with the inhibitor acetazolamide. Authors: Di Fiore, A. / Monti, S.M. / Hilvo, M. / Parkkila, S. / Romano, V. / Scaloni, A. / Pedone, C. / Scozzafava, A. / Supuran, C.T. / De Simone, G. #1: Journal: Proteins / Year: 1988 Title: Refined structure of human carbonic anhydrase II at 2.0 A resolution. Authors: Eriksson, A.E. / Jones, T.A. / Liljas, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3d0n.cif.gz | 136.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3d0n.ent.gz | 104 KB | Display | PDB format |
PDBx/mmJSON format | 3d0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/3d0n ftp://data.pdbj.org/pub/pdb/validation_reports/d0/3d0n | HTTPS FTP |
---|
-Related structure data
Related structure data | 3czvC 1ca2S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 29626.252 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA13 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N1Q1, carbonic anhydrase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.86 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 30% PEG 4000, 0.2 M ammonium acetate, 0.1 M sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.999882 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 1, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999882 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→20 Å / Num. all: 68200 / Num. obs: 68200 / % possible obs: 98.1 % / Redundancy: 3.6 % / Rsym value: 0.058 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 1.55→1.61 Å / Mean I/σ(I) obs: 3.8 / Num. unique all: 6269 / Rsym value: 0.258 / % possible all: 90.3 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CA2 Resolution: 1.55→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→20 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|