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Yorodumi- PDB-4c7g: Structure and activity of the GH20 beta-N-acetylhexosaminidase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c7g | ||||||
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Title | Structure and activity of the GH20 beta-N-acetylhexosaminidase from Streptomyces coelicolor A3(2) | ||||||
Components | BETA-N-ACETYLHEXOSAMINIDASE | ||||||
Keywords | HYDROLASE / BETA-N-ACETYLHEXOSAMINIDASE / N-ACETYLHEXOSAMINIDES / CHITIN DEGRADATION / STREPTOMYCES COELICOLOR | ||||||
Function / homology | Function and homology information glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / ganglioside catabolic process / beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / lysosome / membrane Similarity search - Function | ||||||
Biological species | STREPTOMYCES COELICOLOR (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Nguyenthi, N. / Offen, W.A. / Davies, G.J. / Doucet, N. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Structure and Activity of the Streptomyces Coelicolor A3(2) Beta-N-Acetylhexosaminidase Provides Further Insight Into Gh20 Family Catalysis and Inhibition. Authors: Nguyen Thi, N. / Offen, W.A. / Shareck, F. / Davies, G.J. / Doucet, N. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" 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 | 4c7g.cif.gz | 121.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c7g.ent.gz | 92.8 KB | Display | PDB format |
PDBx/mmJSON format | 4c7g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4c7g_validation.pdf.gz | 455.6 KB | Display | wwPDB validaton report |
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Full document | 4c7g_full_validation.pdf.gz | 457.2 KB | Display | |
Data in XML | 4c7g_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 4c7g_validation.cif.gz | 37.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/4c7g ftp://data.pdbj.org/pub/pdb/validation_reports/c7/4c7g | HTTPS FTP |
-Related structure data
Related structure data | 4c7dSC 4c7fC S: Starting model for refinement 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: 54207.570 Da / Num. of mol.: 1 / Fragment: RESIDUES 42-535 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES COELICOLOR (bacteria) / Strain: A(3)2 / Plasmid: PC109 / Production host: STREPTOMYCES LIVIDANS (bacteria) / Strain (production host): 10-164 / References: UniProt: Q9L068, beta-N-acetylhexosaminidase | ||||
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#2: Chemical | ChemComp-NGO / | ||||
#3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Sequence details | THE FIRST 41 AMINO ACIDS ARE NOT PRESENT IN THE EXPRESSED, SECRETED PROTEIN, AND MAY CONTAIN A ...THE FIRST 41 AMINO ACIDS ARE NOT PRESENT IN THE EXPRESSED, SECRETED PROTEIN, AND MAY CONTAIN A POSSIBLE N-TERMINAL SIGNAL PEPTIDE SEQUENCE. RESIDUE 302 IS MUTATED TO GLN. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | Details: 0.1 M HEPES PH 7.0, 4 % PEG 6000 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 |
Detector | Date: May 19, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→41.35 Å / Num. obs: 50954 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4C7D Resolution: 1.8→71.83 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.537 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.116 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.244 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→71.83 Å
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Refine LS restraints |
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