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- PDB-4lyp: Crystal Structure of Glycoside Hydrolase Family 5 Mannosidase fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4lyp | ||||||
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Title | Crystal Structure of Glycoside Hydrolase Family 5 Mannosidase from Rhizomucor miehei | ||||||
![]() | Exo-beta-1,4-mannosidase | ||||||
![]() | HYDROLASE / Tim Barrel / extracellular protein | ||||||
Function / homology | Glycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / GUANIDINE![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jiang, Z.Q. / Zhou, P. / Yang, S.Q. / Liu, Y. / Yan, Q.J. | ||||||
![]() | ![]() 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 | ![]() | 393 KB | Display | ![]() |
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PDB format | ![]() | 333.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.3 KB | Display | ![]() |
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Full document | ![]() | 472.6 KB | Display | |
Data in XML | ![]() | 44.3 KB | Display | |
Data in CIF | ![]() | 70.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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Unit cell |
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Components
#1: Protein | Mass: 51297.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-GAI / #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | A SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 16% PEG 4000, 0.2 M guanidine hydrochloride, 0.1M HEPES buffer pH 7.5, 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: May 21, 2012 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 | |||||||||
Reflection | Resolution: 1.28→86 Å / Num. all: 235043 / Num. obs: 205153 / % possible obs: 87.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Rmerge(I) obs: 0.052 | |||||||||
Reflection shell |
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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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.159 Å2
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Refinement step | Cycle: LAST / Resolution: 1.28→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.277→1.311 Å / Total num. of bins used: 20
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