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Yorodumi- PDB-1gyh: Structure of D158A Cellvibrio cellulosa alpha-L-arabinanase mutant -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gyh | ||||||
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Title | Structure of D158A Cellvibrio cellulosa alpha-L-arabinanase mutant | ||||||
Components | ARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A | ||||||
Keywords | HYDROLASE / ARABINANASE / PROPELLER / CATALYSIS / CELLVIBRIO / PSEUDOMONAS | ||||||
Function / homology | Function and homology information arabinan endo-1,5-alpha-L-arabinosidase activity / arabinan catabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | CELLVIBRIO CELLULOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Nurizzo, D. / Turkenburg, J.P. / Charnock, S.J. / Roberts, S.M. / Dodson, E.J. / McKie, V.A. / Taylor, E.J. / Gilbert, H.J. / Davies, G.J. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2002 Title: Cellovibrio Cellulosa Alpha-L-Arabinanase 43A Has a Novel Five-Blade Beta-Propeller Fold Authors: Nurizzo, D. / Turkenburg, J.P. / Charnock, S.J. / Roberts, S.M. / Dodson, E.J. / Mckie, V.A. / Taylor, E.J. / Gilbert, H.J. / 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 | 1gyh.cif.gz | 808.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gyh.ent.gz | 672.5 KB | Display | PDB format |
PDBx/mmJSON format | 1gyh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gy/1gyh ftp://data.pdbj.org/pub/pdb/validation_reports/gy/1gyh | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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6 |
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Unit cell |
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-Components
#1: Protein | Mass: 36146.512 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Details: ENGINEERED MUTATION ASP 158 ALA / Source: (gene. exp.) CELLVIBRIO CELLULOSA (bacteria) / Plasmid: PVM1 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): Tuner References: UniProt: P95470*PLUS, arabinan endo-1,5-alpha-L-arabinanase #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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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: 2.2 Å3/Da / Density % sol: 42.9 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 18% PEG5000 MME, 4% AMMONIUM SULFATE, 100MM NA-CACODYLATE PH6.5, 20% GLYCEROL, pH 6.50 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||
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: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 155379 / % possible obs: 97.4 % / Redundancy: 1.89 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.37 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 1.75 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 3.08 / % possible all: 89.8 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Redundancy: 1.9 % |
Reflection shell | *PLUS % possible obs: 89.8 % / Redundancy: 1.8 % / Mean I/σ(I) obs: 3.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MAP FROM AN A P6522 CRYSTAL FORM SOLVED BY MAD Resolution: 1.89→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.191 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R Free: 0.131 / 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: 14.75 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→20 Å
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Refine LS restraints |
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