+Open data
-Basic information
Entry | Database: PDB / ID: 1j9y | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of mannanase 26A from Pseudomonas cellulosa | ||||||
Components | MANNANASE A | ||||||
Keywords | HYDROLASE / TIM BARREL / BETA/ALPHA BARREL / FAMILY 26 GLYCOSIDE HYDROLASE / 4/7-SUPERFAMILY OF GLYCOSIDE HYDROLASES / CLAN GH-A | ||||||
Function / homology | Function and homology information glucomannan metabolic process / galactomannan metabolic process / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / polysaccharide catabolic process Similarity search - Function | ||||||
Biological species | Cellvibrio japonicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.85 Å | ||||||
Authors | Hogg, D. / Woo, E.-J. / Bolam, D.N. / McKie, V.A. / Gilbert, H.J. / Pickersgill, R.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Crystal structure of mannanase 26A from Pseudomonas cellulosa and analysis of residues involved in substrate binding Authors: Hogg, D. / Woo, E.-J. / Bolam, D.N. / McKie, V.A. / Gilbert, H.J. / Pickersgill, R.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1j9y.cif.gz | 95.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1j9y.ent.gz | 69.7 KB | Display | PDB format |
PDBx/mmJSON format | 1j9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j9y_validation.pdf.gz | 415.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1j9y_full_validation.pdf.gz | 416.3 KB | Display | |
Data in XML | 1j9y_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 1j9y_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/1j9y ftp://data.pdbj.org/pub/pdb/validation_reports/j9/1j9y | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 43616.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cellvibrio japonicus (bacteria) / Gene: Man26A / Plasmid: pDB1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: P49424, mannan endo-1,4-beta-mannosidase | ||
---|---|---|---|
#2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.96 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG MME 550, zinc sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8374 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1999 / Details: bent mirror |
Radiation | Monochromator: Triangular monochromator and bent mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8374 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→20 Å / Num. all: 40461 / Num. obs: 40381 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 29.9 |
Reflection shell | Resolution: 1.8→1.85 Å / Rmerge(I) obs: 0.077 / Mean I/σ(I) obs: 10.2 / % possible all: 99.4 |
Reflection shell | *PLUS % possible obs: 99.4 % |
-Processing
Software |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 1.85→12.5 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
| |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→12.5 Å
| |||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||
LS refinement shell | Resolution: 1.85→1.932 Å
| |||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 12.5 Å / σ(F): 0 / Rfactor obs: 0.182 / Rfactor Rfree: 0.2 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS |