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- PDB-6shd: Structure of the GH76A alpha-1,6-mannanase from Salegentibacter s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6shd | ||||||
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Title | Structure of the GH76A alpha-1,6-mannanase from Salegentibacter sp. HEL1_6 | ||||||
![]() | Alpha-1,6-mannanase | ||||||
![]() | HYDROLASE / Mannanase / Glycoside hydrolase / GH76 / CAZyme / Mannan / Carbohydrate | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hehemann, J.H. / Solanki, V. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Glycoside hydrolase from the GH76 family indicates that marine Salegentibacter sp. Hel_I_6 consumes alpha-mannan from fungi. Authors: Solanki, V. / Kruger, K. / Crawford, C.J. / Pardo-Vargas, A. / Danglad-Flores, J. / Hoang, K.L.M. / Klassen, L. / Abbott, D.W. / Seeberger, P.H. / Amann, R.I. / Teeling, H. / Hehemann, J.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 590.2 KB | Display | ![]() |
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PDB format | ![]() | 496.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6shmC ![]() 6y8fC ![]() 3k7xS 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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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 43747.512 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.48 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M Magnesium chloride hexahydrate 0.1 M Sodium acetate pH 5.0 20 % w/v PEG 6000 PH range: 7-8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2→92.02 Å / Num. obs: 87258 / % possible obs: 99.4 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.042 / Rrim(I) all: 0.108 / Net I/σ(I): 11.3 / Num. measured all: 574248 / Scaling rejects: 49 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3K7X Resolution: 2→55.091 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.62 Å2 / Biso mean: 39.0577 Å2 / Biso min: 10.76 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→55.091 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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