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Yorodumi- PDB-4oou: Crystal structure of beta-1,4-D-mannanase from Cryptopygus antarcticus -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oou | ||||||
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Title | Crystal structure of beta-1,4-D-mannanase from Cryptopygus antarcticus | ||||||
Components | Beta-1,4-mannanase | ||||||
Keywords | HYDROLASE / Tim Barrel | ||||||
Function / homology | Function and homology information mannan catabolic process / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / oligosaccharide binding / polysaccharide binding / extracellular region Similarity search - Function | ||||||
Biological species | Cryptopygus antarcticus (arthropod) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å | ||||||
Authors | Kim, M.-K. / An, Y.J. / Jeong, C.-S. / Cha, S.-S. | ||||||
Citation | Journal: Proteins / Year: 2014 Title: Structure-based investigation into the functional roles of the extended loop and substrate-recognition sites in an endo-beta-1,4-d-mannanase from the Antarctic springtail, Cryptopygus antarcticus. Authors: Kim, M.K. / An, Y.J. / Song, J.M. / Jeong, C.S. / Kang, M.H. / Kwon, K.K. / Lee, Y.H. / Cha, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oou.cif.gz | 146.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oou.ent.gz | 121.4 KB | Display | PDB format |
PDBx/mmJSON format | 4oou.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4oou_validation.pdf.gz | 457.5 KB | Display | wwPDB validaton report |
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Full document | 4oou_full_validation.pdf.gz | 473.3 KB | Display | |
Data in XML | 4oou_validation.xml.gz | 29.1 KB | Display | |
Data in CIF | 4oou_validation.cif.gz | 40.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/4oou ftp://data.pdbj.org/pub/pdb/validation_reports/oo/4oou | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 42695.230 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptopygus antarcticus (arthropod) / Production host: Escherichia coli (E. coli) References: UniProt: B4XC07, mannan endo-1,4-beta-mannosidase #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 3.01 Å3/Da / Density % sol: 59.17 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 8.5 Details: 0.1 M Tris-HCl pH 8.5, 25%(w/v) polyethylene glycol (PEG) 3350, microbatch, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 23, 2008 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→50 Å / Num. obs: 37542 / % possible obs: 86.8 % |
Reflection shell | Resolution: 2.36→2.44 Å / % possible all: 77.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→46.16 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.92 / SU B: 9.701 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.323 / ESU R Free: 0.252 / 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: 42.414 Å2
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Refinement step | Cycle: LAST / Resolution: 2.36→46.16 Å
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Refine LS restraints |
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