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- PDB-4qp0: Crystal Structure Analysis of the Endo-1,4-beta-mannanase from Rh... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4qp0 | |||||||||
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Title | Crystal Structure Analysis of the Endo-1,4-beta-mannanase from Rhizomucor miehei | |||||||||
![]() | Endo-beta-mannanase | |||||||||
![]() | HYDROLASE / Tim Barrel / extracellular | |||||||||
Function / homology | ![]() mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zheng, Q.J. / Peng, Z. / Liu, Y. / Yan, Q.J. / Chen, Z.Z. / Qin, Z. | |||||||||
![]() | ![]() Title: Structural insights into the substrate specificity and transglycosylation activity of a fungal glycoside hydrolase family 5 beta-mannosidase. Authors: Zhou, P. / Liu, Y. / Yan, Q. / Chen, Z. / Qin, Z. / Jiang, Z. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.7 KB | Display | ![]() |
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PDB format | ![]() | 63 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.5 KB | Display | ![]() |
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Full document | ![]() | 439.7 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4lypC ![]() 4lyqC ![]() 4lyrC ![]() 4nrrC ![]() 4nrsC ![]() 1qnoS C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 40043.797 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 20-378 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: L7SVX1, mannan endo-1,4-beta-mannosidase |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 80mM NaAc pH 4.6, 1.6M ammonia sulfate, 6% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 11, 2012 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→50 Å / Num. all: 20630 / Num. obs: 18610 / % possible obs: 90.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 31.07 Å2 / Rmerge(I) obs: 0.056 |
Reflection shell | Resolution: 2.26→2.3 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.315 / % possible all: 74 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QNO Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.898 / SU B: 10.053 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.411 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 36.44 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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