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Yorodumi- PDB-8wbu: The crystal structure of circular mannose with mutant H247F of th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wbu | ||||||
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Title | The crystal structure of circular mannose with mutant H247F of the cellobiose 2-epimerase from Caldicellulosiruptor saccharolyticus | ||||||
Components | Cellobiose 2-epimerase | ||||||
Keywords | ISOMERASE / cellobiose 2-epimerase / BIOSYNTHETIC PROTEIN | ||||||
Function / homology | Function and homology information cellobiose epimerase / cellobiose epimerase activity / N-acylglucosamine 2-epimerase activity / sulfoquinovose isomerase activity / N-acetylmannosamine metabolic process / 6-sulfoquinovose(1-) catabolic process to glycerone phosphate and 3-sulfolactaldehyde / N-acetylglucosamine metabolic process / peptidase inhibitor activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Caldicellulosiruptor saccharolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Yang, R.J. / Feng, Y.H. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: The crystal structure of circular mannose with mutant H247F of the cellobiose 2-epimerase from Caldicellulosiruptor saccharolyticus Authors: Yang, R.J. / Feng, Y.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wbu.cif.gz | 186 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wbu.ent.gz | 145.1 KB | Display | PDB format |
PDBx/mmJSON format | 8wbu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wbu_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 8wbu_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8wbu_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 8wbu_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/8wbu ftp://data.pdbj.org/pub/pdb/validation_reports/wb/8wbu | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 46623.121 Da / Num. of mol.: 1 / Mutation: H247F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caldicellulosiruptor saccharolyticus (bacteria) Strain: ATCC 43494 / DSM 8903 / Tp8T 6331 / Gene: Csac_0294 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4XGA6 | ||||
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#2: Sugar | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.8 M NaCl, 0.1 M Tris-HCl pH 8.5, 32% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 193 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 42563 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Net I/σ(I): 13.64 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 2.15 / Num. unique obs: 3127 / CC1/2: 0.678 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→34.851 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.29 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→34.851 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 1.2909 Å / Origin y: -0.3951 Å / Origin z: -8.164 Å
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Refinement TLS group | Selection details: all |