+Open data
-Basic information
Entry | Database: PDB / ID: 1gqi | ||||||
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Title | Structure of Pseudomonas cellulosa alpha-D-glucuronidase | ||||||
Components | ALPHA-GLUCURONIDASE | ||||||
Keywords | GLUCURONIDASE / (ALPHA-BETA)8 BARREL / GLYCOSIDE HYDROLASE | ||||||
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 / SYNCHROTRON / SIRAS / Resolution: 1.48 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 IS ACTUALLY AN 8-STRANDED BARREL THIS IS 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 | 1gqi.cif.gz | 330.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gqi.ent.gz | 265.9 KB | Display | PDB format |
PDBx/mmJSON format | 1gqi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gqi_validation.pdf.gz | 459.7 KB | Display | wwPDB validaton report |
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Full document | 1gqi_full_validation.pdf.gz | 485.8 KB | Display | |
Data in XML | 1gqi_validation.xml.gz | 70.5 KB | Display | |
Data in CIF | 1gqi_validation.cif.gz | 108.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/1gqi ftp://data.pdbj.org/pub/pdb/validation_reports/gq/1gqi | 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) / Plasmid: PTN1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER (DE3) / References: UniProt: B3PC73*PLUS, EC: 3.2.1.139 #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-CO / #4: Chemical | #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 | pH: 8 Details: 30MG/ML, 15% PEG3350, 250MM MGCL2, 5MM TRIS PH8.0, 20% ETHYLENE GLYCOL, 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: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 13, 2001 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.484→20 Å / Num. obs: 235655 / % possible obs: 97.6 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.48→1.56 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 1.6 / % possible all: 90.4 |
Reflection | *PLUS Highest resolution: 1.48 Å / Lowest resolution: 20 Å / Num. obs: 236943 |
Reflection shell | *PLUS Highest resolution: 1.48 Å / % possible obs: 90.4 % / Num. unique obs: 32167 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.48→20 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.779 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.06 / 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: 10.86 Å2
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Refinement step | Cycle: LAST / Resolution: 1.48→20 Å
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