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Yorodumi- PDB-2bjf: Crystal Structure of Conjugated Bile Acid Hydrolase from Clostrid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bjf | ||||||
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Title | Crystal Structure of Conjugated Bile Acid Hydrolase from Clostridium perfringens in Complex with Reaction Products Taurine and Deoxycholate | ||||||
Components | CHOLOYLGLYCINE HYDROLASE | ||||||
Keywords | HYDROLASE / AMIDOHYDROLASE / NTN-HYDROLASE / BILE ACIDS / BSH | ||||||
Function / homology | Function and homology information chenodeoxycholoyltaurine hydrolase activity / choloylglycine hydrolase / choloylglycine hydrolase activity / bile acid biosynthetic process / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides Similarity search - Function | ||||||
Biological species | CLOSTRIDIUM PERFRINGENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | ||||||
Authors | Rossocha, M. / Schultz-Heienbrok, R. / Von Moeller, H. / Coleman, J.P. / Saenger, W. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Conjugated Bile Acid Hydrolase is a Tetrameric N-Terminal Thiol Hydrolase with Specific Recognition of its Cholyl But not of its Tauryl Product Authors: Rossocha, M. / Schultz-Heienbrok, R. / Von Moeller, H. / Coleman, J.P. / Saenger, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bjf.cif.gz | 87.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bjf.ent.gz | 64.9 KB | Display | PDB format |
PDBx/mmJSON format | 2bjf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/2bjf ftp://data.pdbj.org/pub/pdb/validation_reports/bj/2bjf | HTTPS FTP |
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-Related structure data
Related structure data | 2bjgC 3pvaS C: citing same article (ref.) S: Starting model for refinement |
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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: 37221.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Plasmid: PKK233-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P54965, choloylglycine hydrolase | ||
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#2: Chemical | ChemComp-DXC / ( | ||
#3: Chemical | ChemComp-TAU / | ||
#4: Chemical | #5: 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: 2.6 Å3/Da / Density % sol: 51 % |
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Crystal grow | pH: 6 / Details: 2.6M AMMONIUM SULFATE, 100 MM NACITRATE PH 6.0 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9766 |
Detector | Type: MARRESEARCH / Date: Oct 15, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9766 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→50 Å / Num. obs: 42911 / % possible obs: 97 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 29.4 |
Reflection shell | Resolution: 1.67→1.73 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 8 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3PVA Resolution: 1.67→94.07 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.682 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.094 / 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: 14.71 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→94.07 Å
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Refine LS restraints |
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