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Yorodumi- PDB-3civ: Crystal structure of the endo-beta-1,4-mannanase from Alicyclobac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3civ | ||||||
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Title | Crystal structure of the endo-beta-1,4-mannanase from Alicyclobacillus acidocaldarius | ||||||
Components | Endo-beta-1,4-mannanase | ||||||
Keywords | HYDROLASE / TIM BARREL | ||||||
Function / homology | Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / Endo-beta-1,4-mannanase Function and homology information | ||||||
Biological species | Alicyclobacillus acidocaldarius (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.9 Å | ||||||
Authors | Ma, Y. / Zhang, Y. / Xue, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Biochemical and Structural Characterization of the Intracellular Mannanase AaManA of Alicyclobacillus acidocaldarius Reveals a Novel Glycoside Hydrolase Family Belonging to Clan GH-A Authors: Zhang, Y. / Ju, J. / Peng, H. / Gao, F. / Zhou, C. / Zeng, Y. / Xue, Y. / Li, Y. / Henrissat, B. / Gao, G.F. / Ma, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3civ.cif.gz | 79.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3civ.ent.gz | 58.4 KB | Display | PDB format |
PDBx/mmJSON format | 3civ.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3civ_validation.pdf.gz | 419.5 KB | Display | wwPDB validaton report |
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Full document | 3civ_full_validation.pdf.gz | 421.9 KB | Display | |
Data in XML | 3civ_validation.xml.gz | 15 KB | Display | |
Data in CIF | 3civ_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/3civ ftp://data.pdbj.org/pub/pdb/validation_reports/ci/3civ | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38803.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alicyclobacillus acidocaldarius (bacteria) Strain: Tc-12-31 / Gene: AamanA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A5H1I6, mannan endo-1,4-beta-mannosidase |
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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: 1.9 Å3/Da / Density % sol: 35.25 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.2M ammonium dihydrogen phosphate, 0.1M sodium citrate (pH 4.6), VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→35.07 Å / Num. obs: 23386 / % possible obs: 97.3 % / Redundancy: 6.92 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 10.2 / % possible all: 89.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→35.07 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.86 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.146 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.037 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→35.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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