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Open data
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Basic information
Entry | Database: PDB / ID: 6hzx | |||||||||
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Title | Protein-aromatic foldamer complex crystal structure | |||||||||
![]() | Carbonic anhydrase 2 | |||||||||
![]() | LYASE / Protein-Foldamer Complex / Protein-Foldamer interactions / Modified Inhibitor / Anchored Foldamer / Quinoline Oligoamide Foldamer / Benzene Sulfonamide modified inhibitor / Lyase-lyase inhibitor complex | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Post, S. / Langlois d'Estaintot, B. / Fischer, L. / Granier, T. / Huc, I. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 251.4 KB | Display | ![]() |
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PDB format | ![]() | 204.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.2 MB | Display | ![]() |
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Full document | ![]() | 5.1 MB | Display | |
Data in XML | ![]() | 27.9 KB | Display | |
Data in CIF | ![]() | 34.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6q9tC ![]() 3ks3S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / 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: 1 - 257
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 28932.641 Da / Num. of mol.: 2 / Fragment: lyase Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 9 types, 71 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/6H0.gif)
![](data/chem/img/QUK.gif)
![](data/chem/img/ZY9.gif)
![](data/chem/img/QVE.gif)
![](data/chem/img/QVS.gif)
![](data/chem/img/QDD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/6H0.gif)
![](data/chem/img/QUK.gif)
![](data/chem/img/ZY9.gif)
![](data/chem/img/QVE.gif)
![](data/chem/img/QVS.gif)
![](data/chem/img/QDD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-6H0 / ~{ #4: Chemical | ChemComp-QUK / #5: Chemical | ChemComp-ZY9 / #6: Chemical | ChemComp-QVE / #7: Chemical | ChemComp-QVS / #8: Chemical | ChemComp-QDD / #9: Chemical | ChemComp-GOL / #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.82 % / Description: needle |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 6 Details: Ammonium sulfate 0.2M, sodium acetate 0.1M, ph 6.0, PEG 4000 16%, sodium azide 3 mM. HCA 0.3 mM, foldamere 0.3 mM. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 0.980112195015 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.91→44.73 Å / Num. obs: 15735 / % possible obs: 99.8 % / Redundancy: 13.455 % / Biso Wilson estimate: 60.549 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rrim(I) all: 0.097 / Χ2: 1.105 / Net I/σ(I): 19.95 / Num. measured all: 211719 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3KS3 Resolution: 2.91→44.73 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.2055 / WRfactor Rwork: 0.1663 / FOM work R set: 0.8296 / SU Rfree: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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: 1.1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.52 Å2 / Biso mean: 80.678 Å2 / Biso min: 55.41 Å2
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Refinement step | Cycle: final / Resolution: 2.91→44.73 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 8345 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.91→2.986 Å / Rfactor Rfree error: 0 / 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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