[English] 日本語
Yorodumi- PDB-1gqk: Structure of Pseudomonas cellulosa alpha-D-glucuronidase complexe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gqk | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Pseudomonas cellulosa alpha-D-glucuronidase complexed with glucuronic acid | ||||||
Components | ALPHA-D-GLUCURONIDASE | ||||||
Keywords | HYDROLASE / GLUCURONIDASE / (ALPHA-BETA)8 BARREL / GLYCOSIDE HYDROLASE / GLUCURONIC ACID | ||||||
Function / homology | Function and homology information glucuronoxylan catabolic process / xylan alpha-1,2-glucuronosidase / xylan alpha-1,2-glucuronosidase activity / alpha-glucuronidase activity / cell outer membrane / extracellular region Similarity search - Function | ||||||
Biological species | CELLVIBRIO JAPONICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Nurizzo, D. / Nagy, T. / Gilbert, H.J. / Davies, G.J. | ||||||
Citation | Journal: Structure / Year: 2002 Title: The Structural Basis for Catalysis and Specificity of the Pseudomonas Cellulosa Alpha-Glucuronidase, Glca67A Authors: Nurizzo, D. / Nagy, T. / Gilbert, H.J. / Davies, G.J. | ||||||
History |
| ||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" AND "BB" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" AND "BB" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 8-STRANDED BARRELS THESE ARE REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1gqk.cif.gz | 316.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1gqk.ent.gz | 254.5 KB | Display | PDB format |
PDBx/mmJSON format | 1gqk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gqk_validation.pdf.gz | 472.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1gqk_full_validation.pdf.gz | 484 KB | Display | |
Data in XML | 1gqk_validation.xml.gz | 62.7 KB | Display | |
Data in CIF | 1gqk_validation.cif.gz | 95.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/1gqk ftp://data.pdbj.org/pub/pdb/validation_reports/gq/1gqk | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 80439.594 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CELLVIBRIO JAPONICUS (bacteria) / Strain: NCIMB-10462 / Description: NCIMB / Plasmid: PTN1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER (DE3) References: UniProt: Q8VP74, UniProt: B3PC73*PLUS, EC: 3.2.1.139 #2: Sugar | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-CO / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 47.8 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 8 Details: 30MG/ML, 15% PEG3350, 250MM MGCL2, 5MM TRIS PH8.0, 20% ETHYLENE GLYCOL 100MM GLUCURONIC ACID, pH 8.00 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 2001 / Details: OSMICS CONFOCAL MULTILAYER |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 113754 / % possible obs: 97.3 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.2 / % possible all: 94.1 |
Reflection shell | *PLUS % possible obs: 94.1 % / Num. unique obs: 5509 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NATIVE ALPHA-D-GLUCURONIDASE Resolution: 1.9→19.73 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.179 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.67 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→19.73 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|