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Yorodumi- PDB-2cho: Bacteroides thetaiotaomicron hexosaminidase with O-GlcNAcase activity -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cho | ||||||
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Title | Bacteroides thetaiotaomicron hexosaminidase with O-GlcNAcase activity | ||||||
Components | (GLUCOSAMINIDASE) x 2 | ||||||
Keywords | HYDROLASE / O-GLCNACASE / N-ACETYLGLUCOSAMINE | ||||||
Function / homology | Function and homology information protein O-GlcNAcase / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / protein deglycosylation / beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / identical protein binding Similarity search - Function | ||||||
Biological species | BACTEROIDES THETAIOTAOMICRON (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.85 Å | ||||||
Authors | Dennis, R.J. / Taylor, E.J. / Macauley, M.S. / Stubbs, K.A. / Turkenburg, J.P. / Hart, S.J. / Black, G.N. / Vocadlo, D.J. / Davies, G.J. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2006 Title: Structure and Mechanism of a Bacterial B-Glucosaminidase Having O-Glcnacase Activity Authors: Dennis, R.J. / Taylor, E.J. / Macauley, M.S. / Stubbs, K.A. / Turkenburg, J.P. / Hart, S.J. / Black, G.N. / Vocadlo, D.J. / Davies, G.J. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" 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. THE SHEETS PRESENTED AS "BB" 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. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cho.cif.gz | 297.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cho.ent.gz | 239.8 KB | Display | PDB format |
PDBx/mmJSON format | 2cho.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cho_validation.pdf.gz | 460.6 KB | Display | wwPDB validaton report |
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Full document | 2cho_full_validation.pdf.gz | 475.7 KB | Display | |
Data in XML | 2cho_validation.xml.gz | 58.1 KB | Display | |
Data in CIF | 2cho_validation.cif.gz | 88 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/2cho ftp://data.pdbj.org/pub/pdb/validation_reports/ch/2cho | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Details | CHAINS C AND D ARE 2 CHAINS OF UNKNOWN ATOMS AND ARE PARTOF CHAINS A AND B, THEREFORE CHAIN A AND C IS A MONOMERAND NOT A DIMER |
-Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 82330.133 Da / Num. of mol.: 2 / Fragment: RESIDUES 22-737 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria) Strain: VPI-5482 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q89ZI2, beta-N-acetylhexosaminidase #2: Protein/peptide | Mass: 1124.378 Da / Num. of mol.: 2 / Fragment: C TERMINUS, RESIDUES 650-653,660-669 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria) Strain: VPI-5482 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: beta-N-acetylhexosaminidase |
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-Non-polymers , 4 types, 1197 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | RESIDUES IN DISORDERED C TERMINUS MODELLED AS POLYALANINE CHAINS C AND D ARE THE UNKNOWN RESIDUES ...RESIDUES IN DISORDERED |
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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: 2.7 Å3/Da / Density % sol: 54.13 % |
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Crystal grow | pH: 6 Details: 0.5M NA ACETATE, 15% PEG 3500, 0.1M MES, PH6.0 20% GLYCEROL, pH 6.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. obs: 135175 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.85→37.74 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.913 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FOLLOWING POST PROOF-SETTING REVISIONS INFORMED BY THE ANALYSIS PROVIDED BY THE PDB, THE STATISTICS OF THE ACTUALLY COORDINATE FILE ARE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FOLLOWING POST PROOF-SETTING REVISIONS INFORMED BY THE ANALYSIS PROVIDED BY THE PDB, THE STATISTICS OF THE ACTUALLY COORDINATE FILE ARE SLIGHTLY DIFFERENT TO THAT REPORTED IN THE PUBLICATION.
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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: 22.93 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→37.74 Å
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Refine LS restraints |
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