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Yorodumi- PDB-1gxo: Mutant D189A of Family 10 polysaccharide lyase from Cellvibrio ce... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gxo | |||||||||
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Title | Mutant D189A of Family 10 polysaccharide lyase from Cellvibrio cellulosa in complex with trigalaturonic acid | |||||||||
Components | PECTATE LYASE | |||||||||
Keywords | LYASE / PECTATE / ELIMINATION | |||||||||
Function / homology | Function and homology information polysaccharide binding / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / lyase activity Similarity search - Function | |||||||||
Biological species | CELLVIBRIO CELLULOSA (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.05 Å | |||||||||
Authors | Charnock, S.J. / Brown, I.E. / Turkenburg, J.P. / Black, G.W. / Davies, G.J. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: Convergent Evolution Sheds Light on the Anti-Beta-Elimination Mechanism Common to Family 1 and 10 Polysaccharide Lyases Authors: Charnock, S.J. / Brown, I.E. / Turkenburg, J.P. / Black, G.W. / Davies, G.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gxo.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gxo.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 1gxo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/1gxo ftp://data.pdbj.org/pub/pdb/validation_reports/gx/1gxo | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 36667.660 Da / Num. of mol.: 1 / Fragment: CATALYTIC MODULE, RESIDUES 327-649 / Mutation: YES Source method: isolated from a genetically manipulated source Details: COMPLEX WITH TRIGALACTURONIC ACID / Source: (gene. exp.) CELLVIBRIO CELLULOSA (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / Variant (production host): DE3 / References: UniProt: Q9F7L3, pectate lyase |
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#2: Polysaccharide | alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 33 % / Description: DATA INTEGRATED IN CORNERS OF DETECTOR | |||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.2 Details: CRYSTALS OF PEL10ACM WERE GROWN BY VAPOUR-PHASE DIFFUSION USING THE HANGING-DROP METHOD WITH SCREENING AS DESCRIBED BY BRZOZOWSKI & WALTON (2001 [[BRZOZOWSKI, A.M. & WALTON, J.(2001). J. ...Details: CRYSTALS OF PEL10ACM WERE GROWN BY VAPOUR-PHASE DIFFUSION USING THE HANGING-DROP METHOD WITH SCREENING AS DESCRIBED BY BRZOZOWSKI & WALTON (2001 [[BRZOZOWSKI, A.M. & WALTON, J.(2001). J. APPL. CRYST. 34, 97-101.]] ). THE PROTEIN CONCENTRATION WAS 30 MG ML-1 IN NA MES BUFFER PH 5.2 CONTAINING KSCN AT A CONCENTRATION OF 200 MM. THE PRECIPITANT WAS 20%(W/V) MONOMETHYL POLYETHYLENEGLYCOL 2000. 25MM CACL2 AND 20MM TRIGALACTURONIC ACID WERE ALSO ADDED. | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K / Method: vapor diffusion, hanging dropDetails: Charnock, S.J., (2001) Acta Crystallogr., D57, 1141. | |||||||||||||||||||||||||||||||||||
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: ID29 / Wavelength: 0.98 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 14154 / % possible obs: 79.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.1 / % possible all: 29.3 |
Reflection | *PLUS Lowest resolution: 50 Å |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.05→52.7 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.914 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.407 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 17.88 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→52.7 Å
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Refine LS restraints |
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