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Open data
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Basic information
Entry | Database: PDB / ID: 5yll | |||||||||
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Title | Structure of GH113 beta-1,4-mannanase complex with M6. | |||||||||
![]() | beta-1,4-mannanase | |||||||||
![]() | HYDROLASE / Complex | |||||||||
Function / homology | Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / 1,4-beta-xylanase![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Jiang, Z.Q. / You, X. / Yang, S.Q. / Huang, P. / Ma, J.W. | |||||||||
![]() | ![]() Title: Structural insights into the catalytic mechanism of a novel glycoside hydrolase family 113 beta-1,4-mannanase from Amphibacillus xylanus Authors: You, X. / Qin, Z. / Yan, Q. / Yang, S. / Li, Y. / 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 | ![]() | 156.8 KB | Display | ![]() |
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PDB format | ![]() | 121.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 32.7 KB | Display | |
Data in CIF | ![]() | 50 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ylhSC ![]() 5yliC ![]() 5ylkC ![]() 5z4tC S: Starting model for refinement 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36223.473 Da / Num. of mol.: 2 / Mutation: E223A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: NBRC 15112 / Gene: AXY_22370 / Production host: ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG4000, HEPES Na, 2-Propylalcohol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Apr 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→32.75 Å / Num. obs: 68340 / % possible obs: 91 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 45.1 |
Reflection shell | Resolution: 1.81→1.88 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.086 / Mean I/σ(I) obs: 9.4 / Rsym value: 0.082 / % possible all: 91 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5YLH Resolution: 1.81→32.75 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.81→32.75 Å
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LS refinement shell | Highest resolution: 1.81 Å |