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Yorodumi- PDB-5lvs: Self-assembled protein-aromatic foldamer complexes with 2:3 and 2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lvs | |||||||||
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Title | Self-assembled protein-aromatic foldamer complexes with 2:3 and 2:2:1 stoichiometries | |||||||||
Components | Carbonic anhydrase 2 | |||||||||
Keywords | LYASE / PROTEIN-FOLDAMER COMPLEX / PROTEIN FOLDAMER INTERACTIONS / MODIFIED INHIBITOR / ANCHORED FOLDAMER / HCAII DIMERISATION / QUINOLINE OLIGOAMIDE FOLDAMER / BENZENE SULFONAMIDE MODIFIED INHIBITOR / LYASE-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 / regulation of intracellular pH / morphogenesis of an epithelium / 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 / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | |||||||||
Authors | Jewginski, M. / LANGLOIS D'ESTAINTOT, B. / Granier, T. / Huc, Y. | |||||||||
Funding support | Poland, 1items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2017 Title: Self-Assembled Protein-Aromatic Foldamer Complexes with 2:3 and 2:2:1 Stoichiometries. Authors: Jewginski, M. / Granier, T. / Langlois d'Estaintot, B. / Fischer, L. / Mackereth, C.D. / Huc, I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lvs.cif.gz | 266.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lvs.ent.gz | 211.6 KB | Display | PDB format |
PDBx/mmJSON format | 5lvs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/5lvs ftp://data.pdbj.org/pub/pdb/validation_reports/lv/5lvs | HTTPS FTP |
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-Related structure data
Related structure data | 5l3oC 5l6kC 3ks3S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 2 - 260 / Label seq-ID: 1 - 259
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29157.863 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00918, carbonic anhydrase |
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-Non-polymers , 9 types, 604 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-QUK / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-GOL / #8: Chemical | ChemComp-QUJ / #9: Chemical | ChemComp-FOR / | #10: 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: 2.91 Å3/Da / Density % sol: 57.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: Ammonium sulfate 200 mM Sodium acetate 100 mM PEG 4000 24% NaN3 3 mM PH range: 5.2 - 5.35 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97625 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2016 / Details: Kirkpatrick-Baez pair of bi-morph mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: channel cut cryogenically cooled monochromator crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.42→50 Å / Num. obs: 125435 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Biso Wilson estimate: 27.422 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Net I/σ(I): 24.17 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KS3 Resolution: 1.42→45.85 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / SU B: 3.053 / SU ML: 0.049 / SU R Cruickshank DPI: 0.0568 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.053 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.94 Å2 / Biso mean: 27.484 Å2 / Biso min: 11.31 Å2
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Refinement step | Cycle: final / Resolution: 1.42→45.85 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 17620 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.42→1.457 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 0 Å / Origin y: 0 Å / Origin z: 0 Å / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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