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Yorodumi- PDB-1jcz: CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF HUMAN CARBONIC A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jcz | ||||||
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Title | CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF HUMAN CARBONIC ANHYDRASE XII | ||||||
Components | CARBONIC ANHYDRASE XII | ||||||
Keywords | LYASE / Extracellular Domain / Human Carbonic Anhydrase XII / bitopic membrane protein / TYPE I MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information chloride ion homeostasis / estrous cycle / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / basolateral plasma membrane / apical plasma membrane / zinc ion binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Whittington, D.A. / Waheed, A. / Ulmasov, B. / Shah, G.N. / Grubb, J.H. / Sly, W.S. / Christianson, D.W. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: Crystal structure of the dimeric extracellular domain of human carbonic anhydrase XII, a bitopic membrane protein overexpressed in certain cancer tumor cells. Authors: Whittington, D.A. / Waheed, A. / Ulmasov, B. / Shah, G.N. / Grubb, J.H. / Sly, W.S. / Christianson, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jcz.cif.gz | 129 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jcz.ent.gz | 98.5 KB | Display | PDB format |
PDBx/mmJSON format | 1jcz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jcz_validation.pdf.gz | 453.5 KB | Display | wwPDB validaton report |
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Full document | 1jcz_full_validation.pdf.gz | 460 KB | Display | |
Data in XML | 1jcz_validation.xml.gz | 26.4 KB | Display | |
Data in CIF | 1jcz_validation.cif.gz | 38.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/1jcz ftp://data.pdbj.org/pub/pdb/validation_reports/jc/1jcz | HTTPS FTP |
-Related structure data
Related structure data | 1jd0C 1g0eS 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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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a dimer consisting of chains A and B in the asymmetric unit |
-Components
#1: Protein | Mass: 29857.201 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET-11D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O43570, carbonic anhydrase #2: Chemical | #3: Chemical | #4: 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: 2.1 Å3/Da / Density % sol: 41 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: PEG 8000, sodium acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP at 277K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 97 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 8, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→30 Å / Num. all: 80168 / % possible obs: 96.5 % / Redundancy: 5 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 4.1 / % possible all: 79.3 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 80168 / Num. measured all: 402312 |
Reflection shell | *PLUS % possible obs: 79.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1G0E Resolution: 1.55→30 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 519456.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.24 Å2 / ksol: 0.371 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.55→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.65 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 8.1 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 18.9 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.3 / % reflection Rfree: 7.8 % / Rfactor Rwork: 0.256 |