+Open data
-Basic information
Entry | Database: PDB / ID: 6q3o | |||||||||
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Title | PROTEIN-AROMATIC FOLDAMER COMPLEX CRYSTAL STRUCTURE | |||||||||
Components | Carbonic anhydrase 2 | |||||||||
Keywords | LYASE / PROTEIN-FOLDAMER COMPLEX QUINOLINE OPROTEIN-FOLDAMER INTERACTIONSLIGOAMIDE FOLDAMER BENZENE SULFONAMIDE MODIFIED INHIBITOR | |||||||||
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: 2.23 Å | |||||||||
Authors | Zeberko, C. / Langlois d'Estaintot, B. / Fischer, L. / Granier, T. / Kauffmann, B. / Huc, I. | |||||||||
Citation | Journal: To Be Published Title: PROTEIN-AROMATIC FOLDAMER COMPLEX CRYSTAL STRUCTURE Authors: Zeberko, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q3o.cif.gz | 445.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q3o.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6q3o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q3o_validation.pdf.gz | 510.7 KB | Display | wwPDB validaton report |
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Full document | 6q3o_full_validation.pdf.gz | 532.8 KB | Display | |
Data in XML | 6q3o_validation.xml.gz | 55.5 KB | Display | |
Data in CIF | 6q3o_validation.cif.gz | 74.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/6q3o ftp://data.pdbj.org/pub/pdb/validation_reports/q3/6q3o | HTTPS FTP |
-Related structure data
Related structure data | 2ks3 S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 4 - 260 / Label seq-ID: 3 - 259
NCS ensembles :
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 29157.863 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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00918, carbonic anhydrase |
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-Non-polymers , 7 types, 740 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-QNL / ~{ #4: Chemical | ChemComp-QZS / ~{ #5: Chemical | ChemComp-QUK / #6: Chemical | ChemComp-QVE / #7: Chemical | ChemComp-GOL / | #8: 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: 2.75 Å3/Da / Density % sol: 55.46 % / Description: plate |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Zn acetate 0.2 M, Na cacodylate 0.1 M, PEG 8000 18%, NaN3 3mM |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54178 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 9, 2018 / Details: Mirrors Osmic Varimax |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→28.29 Å / Num. obs: 60589 / % possible obs: 99.2 % / Redundancy: 1.89 % / Biso Wilson estimate: 30.3 Å2 / Rsym value: 0.099 / Net I/σ(I): 7.88 |
Reflection shell | Resolution: 2.23→2.33 Å / Redundancy: 1.76 % / Num. unique obs: 7450 / Rsym value: 0.398 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2KS3 2ks3 Resolution: 2.23→28.29 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.899 / SU B: 13.587 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.231 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 31.611 Å2
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Refinement step | Cycle: 1 / Resolution: 2.23→28.29 Å
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Refine LS restraints |
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