+Open data
-Basic information
Entry | Database: PDB / ID: 6q9t | ||||||||||||
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Title | Protein-aromatic foldamer complex crystal structure | ||||||||||||
Components |
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Keywords | LYASE / Protein-Foldamer Complex / Protein-Foldamer interactions / Modified Inhibitor / Anchored Foldamer / 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 / 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) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å | ||||||||||||
Authors | Post, S. / Langlois d'Estaintot, B. / Fischer, L. / Granier, T. / Huc, I. | ||||||||||||
Citation | Journal: Chemistry / Year: 2019 Title: Structure Elucidation of Helical Aromatic Foldamer-Protein Complexes with Large Contact Surface Areas. Authors: Reddy, P.S. / Langlois d'Estaintot, B. / Granier, T. / Mackereth, C.D. / Fischer, L. / Huc, I. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q9t.cif.gz | 124.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q9t.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6q9t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q9t_validation.pdf.gz | 440.9 KB | Display | wwPDB validaton report |
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Full document | 6q9t_full_validation.pdf.gz | 454.9 KB | Display | |
Data in XML | 6q9t_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 6q9t_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/6q9t ftp://data.pdbj.org/pub/pdb/validation_reports/q9/6q9t | HTTPS FTP |
-Related structure data
Related structure data | 6hzxC 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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Unit cell |
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-Components
#1: Protein | Mass: 29157.863 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 BL21(DE3) (bacteria) / References: UniProt: P00918, carbonic anhydrase |
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#2: Protein/peptide | Mass: 3044.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51 % / Description: parallelogram |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: Ammonium sulfate 0.2 M, Sodium acetate 0.1 M pH 5.7, PEG 4000 14%, Sodium azide 3 mM |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980112 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 16, 2018 Details: CRYOGENICALLY COOLED CHANNEL CUT CRYSTAL MONOCHROMATOR, CONVEX PREFOCUSSING MIRROR AND A KIRKPATRICK-BAEZ PAIR OF FOCUSSING MIRRORS |
Radiation | Monochromator: CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.980112 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→45.62 Å / Num. obs: 8622 / % possible obs: 98.6 % / Redundancy: 12.8 % / Biso Wilson estimate: 72.25 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.099 / Net I/σ(I): 17.96 |
Reflection shell | Resolution: 2.68→2.84 Å / Redundancy: 12.64 % / Mean I/σ(I) obs: 2.02 / Num. unique obs: 1262 / CC1/2: 0.859 / Rrim(I) all: 0.99 / % possible all: 91.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KS3 Resolution: 2.68→45.62 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.932 / SU B: 46.885 / SU ML: 0.4 / Cross valid method: THROUGHOUT / ESU R: 2.129 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.834 Å2
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Refinement step | Cycle: 1 / Resolution: 2.68→45.62 Å
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