[English] 日本語
Yorodumi- PDB-1hv1: DISSECTING ELECTROSTATIC INTERACTIONS AND THE PH-DEPENDENT ACTIVI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hv1 | ||||||
---|---|---|---|---|---|---|---|
Title | DISSECTING ELECTROSTATIC INTERACTIONS AND THE PH-DEPENDENT ACTIVITY OF A FAMILY 11 GLYCOSIDASE | ||||||
Components | ENDO-1,4-BETA-XYLANASEXylanase | ||||||
Keywords | HYDROLASE / beta sheet | ||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process Similarity search - Function | ||||||
Biological species | Bacillus circulans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Joshi, M.D. / Sidhu, G. / Nielsen, J.E. / Brayer, G.D. / Withers, S.G. / McIntosh, L.P. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Dissecting the electrostatic interactions and pH-dependent activity of a family 11 glycosidase. Authors: Joshi, M.D. / Sidhu, G. / Nielsen, J.E. / Brayer, G.D. / Withers, S.G. / McIntosh, L.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1hv1.cif.gz | 51.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1hv1.ent.gz | 36.2 KB | Display | PDB format |
PDBx/mmJSON format | 1hv1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/1hv1 ftp://data.pdbj.org/pub/pdb/validation_reports/hv/1hv1 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1hv0C 1bcxS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20351.955 Da / Num. of mol.: 1 / Fragment: Q127A_BCX / Mutation: Q127A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus circulans (bacteria) / Plasmid: PCW / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P09850, endo-1,4-beta-xylanase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.77 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: ammonimu sulphate, sodium chloride, TRIS, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 298 K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Sidhu, G., (1999) Biochemistry, 38, 5346. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 1, 1999 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 17548 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 1.8→1.88 Å / Rmerge(I) obs: 0.115 |
Reflection | *PLUS Lowest resolution: 9999 Å / Num. measured all: 157188 |
Reflection shell | *PLUS Mean I/σ(I) obs: 6.6 |
-Processing
Software |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BCX Resolution: 1.8→10 Å / σ(F): 0
| ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
| ||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||
LS refinement shell | Resolution: 1.8→10 Å
| ||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 10 Å / σ(F): 0 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Rfactor Rwork: 0.164 |