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Yorodumi- PDB-3hbc: Crystal Structure of Choloylglycine Hydrolase from Bacteroides th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hbc | ||||||
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Title | Crystal Structure of Choloylglycine Hydrolase from Bacteroides thetaiotaomicron VPI | ||||||
Components | Choloylglycine hydrolase | ||||||
Keywords | HYDROLASE / alpha-beta sandwich / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Penicillin V Acylase; Chain A / Penicillin V Acylase; Chain A / Choloylglycine hydrolase/NAAA C-terminal / Linear amide C-N hydrolases, choloylglycine hydrolase family / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / hydrolase activity / Alpha Beta / Choloylglycine hydrolase Function and homology information | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.269 Å | ||||||
Authors | Kim, Y. / Bigelow, L. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Choloylglycine Hydrolase from Bacteroides thetaiotaomicron VPI Authors: Kim, Y. / Bigelow, L. / Buck, K. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hbc.cif.gz | 76.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hbc.ent.gz | 61.4 KB | Display | PDB format |
PDBx/mmJSON format | 3hbc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/3hbc ftp://data.pdbj.org/pub/pdb/validation_reports/hb/3hbc | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-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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Details | tetramer, x,y,z -x+1/2,y,-z+3/2 ; translation +1 in z axis x,-y+1/2,-z+3/2 -x+1/2,-y+1/2,z; translation +1 in Z axis |
-Components
#1: Protein | Mass: 36381.418 Da / Num. of mol.: 1 / Fragment: CGH 26-342 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Strain: VPI-5482 / Gene: BT_2086 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 magic / References: UniProt: Q8A600 | ||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-EDO / #4: 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: 2.89 Å3/Da / Density % sol: 57.46 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.05 M Magnesium chloride, 0.1 M HEPES 7.5, 30 % v/v Polyethylene glycol monomethyl ether 550, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 19, 2009 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→42.39 Å / Num. obs: 19843 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 50.22 Å2 / Rsym value: 0.11 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 949 / Rsym value: 0.849 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.269→42.39 Å / SU ML: 1.02 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.185 Å2 / ksol: 0.335 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.269→42.39 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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