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Yorodumi- PDB-1lzv: Site-Specific Mutant (Tyr7 replaced with His) of Human Carbonic A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lzv | ||||||
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Title | Site-Specific Mutant (Tyr7 replaced with His) of Human Carbonic Anhydrase II | ||||||
Components | Carbonic Anhydrase II | ||||||
Keywords | LYASE / Twisted Beta Sheet / Zinc Metalloenzyme | ||||||
Function / homology | Function and homology information positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / morphogenesis of an epithelium / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / one-carbon metabolic process / apical part of cell / myelin sheath / zinc ion binding / extracellular exosome / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Tu, C.K. / Qian, M. / An, H. / Wadhwa, N.R. / Duda, D.M. / Yoshioka, C. / Pathak, Y. / McKenna, R. / Laipis, P.J. / Silverman, D.N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Kinetic analysis of multiple proton shuttles in the active site of human carbonic anhydrase. Authors: Tu, C. / Qian, M. / An, H. / Wadhwa, N.R. / Duda, D. / Yoshioka, C. / Pathak, Y. / McKenna, R. / Laipis, P.J. / Silverman, D.N. | ||||||
History |
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Remark 999 | SEQUENCE Residue 125 is covalently bound to 127. Number 126 is not used as a matter of convention ...SEQUENCE Residue 125 is covalently bound to 127. Number 126 is not used as a matter of convention for sequence alignments. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lzv.cif.gz | 64.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lzv.ent.gz | 46.5 KB | Display | PDB format |
PDBx/mmJSON format | 1lzv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lzv_validation.pdf.gz | 423.1 KB | Display | wwPDB validaton report |
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Full document | 1lzv_full_validation.pdf.gz | 425.4 KB | Display | |
Data in XML | 1lzv_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 1lzv_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lz/1lzv ftp://data.pdbj.org/pub/pdb/validation_reports/lz/1lzv | HTTPS FTP |
-Related structure data
Related structure data | 1g0fS 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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Details | The Biological Assembly is a Monomer Constructed from Chain A |
-Components
#1: Protein | Mass: 29264.035 Da / Num. of mol.: 1 / Mutation: Y7H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P00918, carbonic anhydrase |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.73 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: Ammonium Sulfate, Tris HCL, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 40 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.548 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 10, 2002 |
Radiation | Monochromator: Osmic Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.548 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 11305 / % possible obs: 85 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.151 |
Reflection shell | Resolution: 2.3→2.38 Å / % possible all: 85 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Num. obs: 9586 / Rmerge(I) obs: 0.151 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / % possible obs: 87.3 % / Num. unique obs: 979 / Rmerge(I) obs: 0.401 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G0F Resolution: 2.3→19.94 Å / Rfactor Rfree error: 0.011 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.3849 Å2 / ksol: 0.342336 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.7 Å2
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Refine analyze | Luzzati coordinate error free: 0.32 Å / Luzzati sigma a free: 0.35 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→19.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.248 / Rfactor Rwork: 0.184 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.401 |