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Yorodumi- PDB-4a3z: CpGH89CBM32-4 (seleno-methionine labeled) produced by Clostridium... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a3z | ||||||
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Title | CpGH89CBM32-4 (seleno-methionine labeled) produced by Clostridium perfringens | ||||||
Components | ALPHA-N-ACETYLGLUCOSAMINIDASE FAMILY PROTEIN | ||||||
Keywords | HYDROLASE / FAMILY 32 CARBOHYDRATE-BINDING MODULE | ||||||
Function / homology | Function and homology information hydrolase activity, acting on glycosyl bonds / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | CLOSTRIDIUM PERFRINGENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å | ||||||
Authors | Ficko-Blean, E. / Stuart, C.P. / Suits, M.D. / Cid, M. / Tessier, M. / Woods, R.J. / Boraston, A.B. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Carbohydrate Recognition by an Architecturally Complex Alpha-N-Acetylglucosaminidase from Clostridium Perfringens. Authors: Ficko-Blean, E. / Stuart, C.P. / Suits, M.D. / Cid, M. / Tessier, M. / Woods, R.J. / Boraston, A.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a3z.cif.gz | 75.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a3z.ent.gz | 60.6 KB | Display | PDB format |
PDBx/mmJSON format | 4a3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/4a3z ftp://data.pdbj.org/pub/pdb/validation_reports/a3/4a3z | HTTPS FTP |
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-Related structure data
Related structure data | 4a41C 4a42C 4a44C 4a45C 4a6oC 4aaxC 4a40 4a43 C: citing same article (ref.) |
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Similar 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: 17755.682 Da / Num. of mol.: 1 / Fragment: CBM32-4, RESIDUES 1206-1343 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR References: UniProt: Q0TST1, UniProt: A0A0H2YU91*PLUS, alpha-N-acetylglucosaminidase |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.14 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9796 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→20 Å / Num. obs: 23846 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 16.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.55→1.64 Å / Redundancy: 16.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 7.6 / % possible all: 99.8 |
-Processing
Software | Name: REFMAC / Version: 5.5.0109 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.55→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.032 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.066 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.582 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→20 Å
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Refine LS restraints |
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