+Open data
-Basic information
Entry | Database: PDB / ID: 1c93 | ||||||
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Title | Endo-Beta-N-Acetylglucosaminidase H, D130N/E132Q Double Mutant | ||||||
Components | ENDO-BETA-N-ACETYLGLUCOSAMINIDASE H | ||||||
Keywords | HYDROLASE / (BETA/ALPHA)8 BARREL | ||||||
Function / homology | Function and homology information mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Streptomyces plicatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | Rao, V. / Cui, T. / Guan, C. / Van Roey, P. | ||||||
Citation | Journal: Protein Sci. / Year: 1999 Title: Mutations of endo-beta-N-acetylglucosaminidase H active site residues Asp130 and Glu132: activities and conformations. Authors: Rao, V. / Cui, T. / Guan, C. / Van Roey, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c93.cif.gz | 63.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c93.ent.gz | 47.2 KB | Display | PDB format |
PDBx/mmJSON format | 1c93.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c93_validation.pdf.gz | 391.1 KB | Display | wwPDB validaton report |
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Full document | 1c93_full_validation.pdf.gz | 398.9 KB | Display | |
Data in XML | 1c93_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 1c93_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/1c93 ftp://data.pdbj.org/pub/pdb/validation_reports/c9/1c93 | HTTPS FTP |
-Related structure data
Related structure data | 1c3fC 1c8xC 1c8yC 1c90C 1c91C 1c92C 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
#1: Protein | Mass: 28523.443 Da / Num. of mol.: 1 / Mutation: D130N AND E132Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces plicatus (bacteria) / Plasmid: PMAL / Production host: Escherichia coli (E. coli) References: UniProt: P04067, mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.86 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 34% PEG1500, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 39207 / Num. obs: 12430 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.083 |
Reflection shell | Resolution: 2.1→2.2 Å / % possible all: 92.3 |
Reflection | *PLUS % possible obs: 96.52 % / Redundancy: 3.15 % / Num. measured all: 39207 / Rmerge(I) obs: 0.093 |
Reflection shell | *PLUS % possible obs: 92.3 % |
-Processing
Software |
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Refinement | Resolution: 2.1→10 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.1→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.205 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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