[English] 日本語
Yorodumi- PDB-8wbv: The crystal structure of linear mannose with mutant H247F of the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wbv | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of linear 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: 1.95 Å | ||||||
Authors | Yang, R.J. / Feng, Y.H. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: To Be Published Title: The crystal structure of linear mannose with mutant H247F of the cellobiose 2-epimerase from Caldicellulosiruptor saccharolyticus Authors: Yang, R.J. / Feng, Y.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8wbv.cif.gz | 184 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8wbv.ent.gz | 143.2 KB | Display | PDB format |
PDBx/mmJSON format | 8wbv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wbv_validation.pdf.gz | 804.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8wbv_full_validation.pdf.gz | 807 KB | Display | |
Data in XML | 8wbv_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 8wbv_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/8wbv ftp://data.pdbj.org/pub/pdb/validation_reports/wb/8wbv | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 |
---|---|
#2: Sugar | ChemComp-DNO / |
#3: Sugar | ChemComp-BMA / |
#4: Chemical | ChemComp-EDO / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.12 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.8M NaCl,0.1Tris-HCI pH 8.5, 32% PEG3350 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
---|---|
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: 1.95→50 Å / Num. obs: 28308 / % possible obs: 92 % / Observed criterion σ(I): -3 / Redundancy: 3.27 % / CC1/2: 0.995 / Rmerge(I) obs: 0.084 / Net I/σ(I): 11.35 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 3.62 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 2.44 / Num. unique obs: 2179 / CC1/2: 0.807 / % possible all: 96.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→29.877 Å / SU ML: 0.23 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 21.72 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→29.877 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 27.0411 Å / Origin y: 1.0133 Å / Origin z: -9.3553 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |