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Yorodumi- PDB-1gqj: Structure of Pseudomonas cellulosa alpha-D-glucuronidase complexe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gqj | |||||||||
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Title | Structure of Pseudomonas cellulosa alpha-D-glucuronidase complexed with xylobiose | |||||||||
Components | ALPHA-D-GLUCURONIDASE | |||||||||
Keywords | GLUCURONIDASE / (ALPHA-BETA)8 BARREL / GLYCOSIDE HYDROLASE / XYLOBIOSE | |||||||||
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 | PSEUDOMONAS CELLULOSA (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 |
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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 |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gqj.cif.gz | 322.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gqj.ent.gz | 258.7 KB | Display | PDB format |
PDBx/mmJSON format | 1gqj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gqj_validation.pdf.gz | 974.6 KB | Display | wwPDB validaton report |
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Full document | 1gqj_full_validation.pdf.gz | 999 KB | Display | |
Data in XML | 1gqj_validation.xml.gz | 66.4 KB | Display | |
Data in CIF | 1gqj_validation.cif.gz | 100.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/1gqj ftp://data.pdbj.org/pub/pdb/validation_reports/gq/1gqj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 80439.594 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS CELLULOSA (bacteria) / Strain: NCIMB-10462 / Plasmid: PTN1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER (DE3) / References: UniProt: B3PC73*PLUS, EC: 3.2.1.139 #2: Polysaccharide | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-CO / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 47.8 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8 Details: 30MG/ML, 15% PEG3350, 250MM MGCL2, 5MM TRIS PH8.0, 20% ETHYLENE GLYCOL 100MM XYLOTRIOSE, pH 8.00 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 2001 / Details: MSC/RIGAKU FOCUSSING MIRRORS |
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: 109005 / % possible obs: 95 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.1 / % possible all: 93.4 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 108980 |
Reflection shell | *PLUS % possible obs: 93.4 % / Num. unique obs: 5331 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NATIVE ALPHA-D-GLUCURONIDASE Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.964 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 17.64 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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