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- PDB-5fnk: Native state mass spectrometry, surface plasmon resonance and X-r... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fnk | ||||||
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Title | Native state mass spectrometry, surface plasmon resonance and X-ray crystallography correlate strongly as a fragment screening combination | ||||||
![]() | CARBONIC ANHYDRASE 2 | ||||||
![]() | LYASE / FRAGMENTS / CARBONIC ANHYDRASE / METALLOPROTEIN | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Woods, L.A. / Dolezal, O. / Ren, B. / Ryan, J.H. / Peat, T.S. / Poulsen, S.A. | ||||||
![]() | ![]() Title: Native State Mass Spectrometry, Surface Plasmon Resonance and X-Ray Crystallography Correlate Strongly as a Fragment Screening Combination. Authors: Woods, L. / Dolezal, O. / Ren, B. / Ryan, J.H. / Peat, T.S. / Poulsen, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.8 KB | Display | ![]() |
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PDB format | ![]() | 55.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.7 KB | Display | ![]() |
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Full document | ![]() | 467.2 KB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 23.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5eh5C ![]() 5eh7C ![]() 5eh8C ![]() 5ehvC ![]() 5ehwC ![]() 5floC ![]() 5flpC ![]() 5flqC ![]() 5flrC ![]() 5flsC ![]() 5fltC ![]() 5fngC ![]() 5fnhC ![]() 5fniC ![]() 5fnjC ![]() 5fnlC ![]() 5fnmC ![]() 4cq0S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29289.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 289 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/5OO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/5OO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | ChemComp-DMS / | ||||
#4: Chemical | ChemComp-ACY / | ||||
#5: Chemical | #6: Chemical | ChemComp-5OO / (~{ | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.4 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 8.5 Details: 15 MG/ML PROTEIN WITH 2.7 M AMMONIUM SULFATE, 100 MM TRIS PH 8.5 AT 8 C IN SITTING DROPS. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→41.5 Å / Num. obs: 33070 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.59→1.61 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.9 / % possible all: 90.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4CQ0 Resolution: 1.59→69.88 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.604 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY DENSITY FOR FRAGMENT IS WEAKER THAN MOST OF THE OTHERS AND ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY DENSITY FOR FRAGMENT IS WEAKER THAN MOST OF THE OTHERS AND THE COMPOUND IS MODELLED AT 0.8 OCCUPANCY
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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: 14.128 Å2
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Refinement step | Cycle: LAST / Resolution: 1.59→69.88 Å
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Refine LS restraints |
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