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- PDB-3pzi: Structure of the hyperthermostable endo-1,4-beta-D-mannanase from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3pzi | ||||||
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Title | Structure of the hyperthermostable endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 in complex with beta-D-glucose | ||||||
![]() | Mannan endo-1,4-beta-mannosidase. Glycosyl Hydrolase family 5 | ||||||
![]() | HYDROLASE / alpha/beta barrel / glycosyl hydrolase / sugar binding / secreted | ||||||
Function / homology | ![]() mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / metabolic process Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Santos, C.R. / Meza, A.N. / Paiva, J.H. / Silva, J.C. / Ruller, R. / Prade, R.A. / Squina, F.M. / Murakami, M.T. | ||||||
![]() | ![]() Title: Structural characterization of a novel hyperthermostable endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 Authors: Santos, C.R. / Meza, A.N. / Paiva, J.H. / Silva, J.C. / Ruller, R. / Prade, R.A. / Squina, F.M. / Murakami, M.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172.9 KB | Display | ![]() |
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PDB format | ![]() | 136.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.4 KB | Display | ![]() |
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Full document | ![]() | 452.4 KB | Display | |
Data in XML | ![]() | 18.9 KB | Display | |
Data in CIF | ![]() | 29.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3pz9C ![]() 3pzgC ![]() 3pzmC ![]() 3pznC ![]() 3pzoC ![]() 3pzqC C: citing same article ( |
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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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Unit cell |
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Components
#1: Protein | Mass: 44213.379 Da / Num. of mol.: 1 / Fragment: UNP residues 32-393 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A5IMX7, mannan endo-1,4-beta-mannosidase |
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#2: Sugar | ChemComp-BGC / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.7 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.8 M phosphate, 0.2 M sodium chloride, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 10, 2010 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.4586 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→35.4 Å / Num. obs: 62462 / % possible obs: 99.9 % / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.55→1.61 Å / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 17.022 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→35.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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