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- PDB-8bry: Room-temperature structure of Pedobacter heparinus N-acetylglucos... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8bry | ||||||
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Title | Room-temperature structure of Pedobacter heparinus N-acetylglucosamine 2-epimerase at atmospheric pressure | ||||||
![]() | N-acylglucosamine 2-epimerase | ||||||
![]() | ISOMERASE / HPMX / high-pressure macromolecular crystallography / sapphire capillary / room temperature / sialic acid synthesis / (alpha/alpha)6 barrel | ||||||
Function / homology | ![]() N-acylglucosamine 2-epimerase / N-acylglucosamine 2-epimerase activity / sulfoquinovose isomerase activity / 6-sulfoquinovose(1-) catabolic process to glycerone phosphate and 3-sulfolactaldehyde / N-acetylmannosamine metabolic process / N-acetylglucosamine metabolic process / peptidase inhibitor activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lieske, J. / Saouane, S. / Assmann, M. / Zaun, H. / Kuballa, J. / Meents, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: High-pressure macromolecular crystallography to explore the conformational space of proteins Authors: Lieske, J. / Saouane, S. / Guenther, S. / Reinke, P.Y.A. / Falke, S. / Ewert, W. / Meyer, J. / Pakendorf, T. / Reime, B. / Burkhardt, A. / Crosas, E. / Hakanpaeae, J. / Stachnik, K. / Sieg, ...Authors: Lieske, J. / Saouane, S. / Guenther, S. / Reinke, P.Y.A. / Falke, S. / Ewert, W. / Meyer, J. / Pakendorf, T. / Reime, B. / Burkhardt, A. / Crosas, E. / Hakanpaeae, J. / Stachnik, K. / Sieg, J. / Rarey, M. / Assmann, M. / Zaun, H. / Kuballa, J. / Chapman, H.N. / Meents, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 586 KB | Display | ![]() |
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PDB format | ![]() | 401.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.7 KB | Display | ![]() |
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Full document | ![]() | 447.6 KB | Display | |
Data in XML | ![]() | 32.5 KB | Display | |
Data in CIF | ![]() | 48.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8brzC ![]() 8bs0C ![]() 8bs1C ![]() 8bs2C ![]() 2gz6S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 48868.938 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.57 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 12.6 mg/ml protein in 20 mM sodium phosphate buffer pH 7.5 were mixed (4+2 ul) with 0.1 M sodium cacodylate buffer pH 5.0, 0.35 M sodium acetate and 26% PEG 8000. Crystals grew at room temperature in 5-7 days. Pressure: 101.325 kPa |
-Data collection
Diffraction | Ambient environment: air / Ambient pressure: 101.325 kPa / Mean temperature: 295 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 X CdTe 2M / Detector: PIXEL / Date: Jun 15, 2020 |
Diffraction measurement | Specimen support: kapton loop |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.477 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→17.62 Å / Num. obs: 135935 / % possible obs: 99.67 % / Redundancy: 6.8 % / Biso Wilson estimate: 20.38 Å2 / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.07439 / Rrim(I) all: 0.1914 / Net I/σ(I): 5.83 |
Reflection shell | Resolution: 1.5→1.554 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.755 / Mean I/σ(I) obs: 0.89 / Num. unique obs: 13529 / CC1/2: 0.495 / CC star: 0.814 / Rpim(I) all: 0.7352 / Rrim(I) all: 1.905 / % possible all: 99.29 |
Cell measurement | Pressure: 101.325 kPa |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2GZ6 Resolution: 1.5→17.62 Å / SU ML: 0.1743 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.4047 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→17.62 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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