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Yorodumi- PDB-5l9e: CRYSTAL STRUCTURE OF HUMAN CARBONIC ANHYDRASE II IN COMPLEX WITH ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l9e | |||||||||
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Title | CRYSTAL STRUCTURE OF HUMAN CARBONIC ANHYDRASE II IN COMPLEX WITH A QUINOLINE OLIGOAMIDE FOLDAMER | |||||||||
Components | Carbonic anhydrase 2 | |||||||||
Keywords | Lyase/Inhibitor / PROTEIN-FOLDAMER COMPLEX / PROTEIN FOLDAMER INTERACTIONS / MODIFIED INHIBITOR / ANCHORED FOLDAMER / HCAII DIMERISATION / QUINOLINE OLIGOAMIDE FOLDAMER / BENZENE SULFONAMIDE MODIFIED INHIBITOR / LYASE-INHIBITOR COMPLEX | |||||||||
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 / molecular replacement / Resolution: 2.9 Å | |||||||||
Authors | Vallade, M. / Langlois d'Estaintot, B. / Granier, T. / Huc, I. | |||||||||
Citation | Journal: To Be Published Title: CRYSTAL STRUCTURE OF HUMAN CARBONIC ANHYDRASE II IN COMPLEX WITH A QUINOLINE OLIGOAMIDE FOLDAMER Authors: Vallade, M. / Fischer, L. / Langlois d'Estaintot, B. / Granier, T. / Huc, I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l9e.cif.gz | 442.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l9e.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5l9e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l9e_validation.pdf.gz | 503 KB | Display | wwPDB validaton report |
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Full document | 5l9e_full_validation.pdf.gz | 538.9 KB | Display | |
Data in XML | 5l9e_validation.xml.gz | 47 KB | Display | |
Data in CIF | 5l9e_validation.cif.gz | 61.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/5l9e ftp://data.pdbj.org/pub/pdb/validation_reports/l9/5l9e | HTTPS FTP |
-Related structure data
Related structure data | 5l6tC 5l70C 3ks3S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 29289.062 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: PET11D / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00918, carbonic anhydrase |
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-Non-polymers , 6 types, 211 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-6H0 / ~{ #4: Chemical | ChemComp-QUJ / #5: Chemical | ChemComp-QVE / #6: Chemical | ChemComp-GOL / #7: 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: 2.82 Å3/Da / Density % sol: 56.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1 / Details: ZnOAc, NaCac, PEG 8000, NaN3 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 18, 2015 / Details: Kirkpatrick-Baez pair of bi-morph mirrors | |||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.89→85.39 Å / Num. obs: 28671 / % possible obs: 98.1 % / Redundancy: 3.1 % / CC1/2: 0.964 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.111 / Rrim(I) all: 0.204 / Net I/σ(I): 5.6 / Num. measured all: 88990 / Scaling rejects: 248 | |||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KS3 Resolution: 2.9→85.39 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.872 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.585 / ESU R Free: 0.452 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 124.17 Å2 / Biso mean: 63.01 Å2 / Biso min: 45.25 Å2
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Refinement step | Cycle: final / Resolution: 2.9→85.39 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.895→2.97 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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