+Open data
-Basic information
Entry | Database: PDB / ID: 6lv3 | ||||||
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Title | Co- Carbonic Anhydrase II pH 11.0 0 atm CO2 | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | METAL BINDING PROTEIN / LYASE / metalloenzymes / carbonic anhydrase / enzyme mechanism / metal coordination geometry / proton transfer / biological water dynamics | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Kim, C.U. / Kim, J.K. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Nat Commun / Year: 2020 Title: Elucidating the role of metal ions in carbonic anhydrase catalysis. Authors: Kim, J.K. / Lee, C. / Lim, S.W. / Adhikari, A. / Andring, J.T. / McKenna, R. / Ghim, C.M. / Kim, C.U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lv3.cif.gz | 211.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lv3.ent.gz | 163.5 KB | Display | PDB format |
PDBx/mmJSON format | 6lv3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lv3_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6lv3_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6lv3_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 6lv3_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/6lv3 ftp://data.pdbj.org/pub/pdb/validation_reports/lv/6lv3 | HTTPS FTP |
-Related structure data
Related structure data | 6luuC 6luvC 6luwC 6luxC 6luyC 6luzC 6lv1C 6lv2C 6lv4C 6lv5C 6lv6C 6lv7C 6lv8C 6lv9C 6lvaC 5yukS 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: 29289.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-CO / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 11 / Details: 1.3 M sodium citrate, 50 mM Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 17, 2019 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→30 Å / Num. obs: 71904 / % possible obs: 95 % / Redundancy: 7.6 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.033 / Rrim(I) all: 0.091 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 3443 / CC1/2: 0.909 / CC star: 0.976 / Rpim(I) all: 0.179 / Rrim(I) all: 0.497 / % possible all: 91.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YUK Resolution: 1.2→30 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.916 / SU ML: 0.019 / Cross valid method: FREE R-VALUE / ESU R: 0.035 / ESU R Free: 0.035 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.94 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→30 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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