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- PDB-4nrs: Crystal Structure of Glycoside Hydrolase Family 5 Mannosidase (E2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4nrs | |||||||||
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Title | Crystal Structure of Glycoside Hydrolase Family 5 Mannosidase (E202A mutant) from Rhizomucor miehei in complex with mannobiose | |||||||||
![]() | Exo-beta-1,4-mannosidase | |||||||||
![]() | HYDROLASE / Tim Barrel / extracellular protein | |||||||||
Function / homology | ![]() beta-mannosidase activity / mannan endo-1,4-beta-mannosidase / metabolic process Similarity search - Function | |||||||||
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 | ![]() | 176.8 KB | Display | ![]() |
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PDB format | ![]() | 144.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 32.5 KB | Display | |
Data in CIF | ![]() | 46.8 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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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 51239.926 Da / Num. of mol.: 2 / Mutation: E202A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Water | ChemComp-HOH / | Sequence details | A SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THERE IS MUTATION E202A. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10% mannobiose, 16% PEG 4000 (w/v), 200mM GdnHCl, 100mM 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: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.57→87.92 Å / Num. all: 28430 / Num. obs: 27497 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.099 / Rsym value: 0.096 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.36 / Num. unique all: 1297 / Rsym value: 0.394 / % possible all: 88.3 |
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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: 30.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2.57→50 Å
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Refine LS restraints |
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