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- PDB-6zbx: Structure of the catalytic domain of the Bacillus circulans alpha... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zbx | |||||||||
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Title | Structure of the catalytic domain of the Bacillus circulans alpha-1,6 Mannanase in complex with an alpha-1,6- alpha-manno-cyclophellitol carbasugar-stabilised trisaccharide inhibitor | |||||||||
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Function / homology | ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Schroeder, S. / Offen, W.A. / Jin, Y. / De Boer, C. / Enoterpi, J. / Marino, L. / van der Marel, G.A. / Codee, J.D.C. / Overkleeft, H.S. / Davies, G.J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Development of Non-Hydrolysable Oligosaccharide Activity-Based Inactivators for Endoglycanases: A Case Study on alpha-1,6 Mannanases. Authors: Schroder, S.P. / Offen, W.A. / Males, A. / Jin, Y. / de Boer, C. / Enotarpi, J. / Marino, L. / van der Marel, G.A. / Florea, B.I. / Codee, J.D.C. / Overkleeft, H.S. / Davies, G.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 309.5 KB | Display | ![]() |
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PDB format | ![]() | 246.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6zbmC ![]() 6zbwC ![]() 7nl5C ![]() 4d4aS 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
-Protein / Protein/peptide / Sugars , 3 types, 5 molecules ABE![](data/chem/img/MAN.gif)
![](data/chem/img/MAN.gif)
#1: Protein | Mass: 40930.859 Da / Num. of mol.: 2 / Mutation: R341Q Source method: isolated from a genetically manipulated source Details: N-terminally His-tagged catalytic domain of BcGH76 with mutation R341Q Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | | Mass: 358.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Peptide, probably connected to either chain A or B, but unable to be identified Source: (gene. exp.) ![]() ![]() ![]() ![]() #6: Sugar | ![]() |
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-Non-polymers , 4 types, 589 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/PBW.gif)
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![](data/chem/img/HOH.gif)
![](data/chem/img/PBW.gif)
![](data/chem/img/M96.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ![]() #4: Chemical | #5: Chemical | #7: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.01 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, ammonium nitrate |
-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: Feb 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.35→50.49 Å / Num. obs: 127986 / % possible obs: 95.1 % / Redundancy: 3.5 % / CC1/2: 0.977 / Rpim(I) all: 0.026 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 3 % / Num. unique obs: 5907 / CC1/2: 0.638 / Rpim(I) all: 0.398 / % possible all: 88.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4D4A.PDB Resolution: 1.35→50.49 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.458 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: THERE ARE REGIONS OF UNMODELLED DENSITY NEAR THE SIDE CHAINS OF PHE122A, ASN206A AND 206B, ASP266A AND TYR319A. THERE IS A PEPTIDE CHAIN OF 4 AMINO ACIDS WHICH COULD NOT BE ASSIGNED WITH ...Details: THERE ARE REGIONS OF UNMODELLED DENSITY NEAR THE SIDE CHAINS OF PHE122A, ASN206A AND 206B, ASP266A AND TYR319A. THERE IS A PEPTIDE CHAIN OF 4 AMINO ACIDS WHICH COULD NOT BE ASSIGNED WITH CONFIDENCE TO EITHER CHAIN A OR B AND HAVE THEREFORE BEEN MODELLED AS UNK RESIDUES.
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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 max: 71.97 Å2 / Biso mean: 16.658 Å2 / Biso min: 7.99 Å2
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Refinement step | Cycle: final / Resolution: 1.35→50.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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