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- PDB-2zun: Functional Analysis of Hyperthermophilic Endocellulase from the A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zun | |||||||||
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Title | Functional Analysis of Hyperthermophilic Endocellulase from the Archaeon Pyrococcus horikoshii | |||||||||
![]() | 458aa long hypothetical endo-1,4-beta-glucanase | |||||||||
![]() | HYDROLASE / TIM BARREL | |||||||||
Function / homology | ![]() hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kim, H.-W. / Ishikawa, K. | |||||||||
![]() | ![]() Title: Functional Analysis of Hyperthermophilic Endocellulase from the Archaeon Pyrococcus horikoshii Authors: Kim, H.-W. / Ishikawa, K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 251.7 KB | Display | ![]() |
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PDB format | ![]() | 202.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.6 MB | Display | |
Data in XML | ![]() | 53 KB | Display | |
Data in CIF | ![]() | 74.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zumS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 51954.863 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THERE IS CONFLICT BETWEEN THE REPORTED SEQUENCE AND THE DATABASE REFERENCE SEQUENCE. IN THIS ENTRY, ...THERE IS CONFLICT BETWEEN THE REPORTED SEQUENCE AND THE DATABASE REFERENCE SEQUENCE. IN THIS ENTRY, 289TH RESIDUE IS OBVIOUSLY LYS BASED ON THE ELECTRON DENSITY. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 38.01 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.5M ammonium phosphate, 0.1M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: Bruker DIP-6040 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 97064 / Num. obs: 94740 / % possible obs: 97.6 % / Redundancy: 3.5 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2ZUM Resolution: 2→48.37 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.385 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.196 / 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 / Bsol: 73.825 Å2 | |||||||||||||||||||||
Displacement parameters | Biso max: 84.75 Å2 / Biso mean: 37.085 Å2 / Biso min: 9.12 Å2
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Refinement step | Cycle: LAST / Resolution: 2→48.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Xplor file |
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