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- PDB-4mb4: Crystal structure of E153Q mutant of cold-adapted chitinase from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4mb4 | |||||||||
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Title | Crystal structure of E153Q mutant of cold-adapted chitinase from Moritella complex with Nag4 | |||||||||
![]() | Chitinase 60![]() | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Malecki, P.H. / Vorgias, C.E. / Rypniewski, W. | |||||||||
![]() | ![]() Title: Crystal structures of substrate-bound chitinase from the psychrophilic bacterium Moritella marina and its structure in solution. Authors: Piotr H Malecki / Constantinos E Vorgias / Maxim V Petoukhov / Dmitri I Svergun / Wojciech Rypniewski / ![]() ![]() ![]() Abstract: The four-domain structure of chitinase 60 from Moritella marina (MmChi60) is outstanding in its complexity. Many glycoside hydrolases, such as chitinases and cellulases, have multi-domain structures, ...The four-domain structure of chitinase 60 from Moritella marina (MmChi60) is outstanding in its complexity. Many glycoside hydrolases, such as chitinases and cellulases, have multi-domain structures, but only a few have been solved. The flexibility of the hinge regions between the domains apparently makes these proteins difficult to crystallize. The analysis of an active-site mutant of MmChi60 in an unliganded form and in complex with the substrates NAG4 and NAG5 revealed significant differences in the substrate-binding site compared with the previously determined complexes of most studied chitinases. A SAXS experiment demonstrated that in addition to the elongated state found in the crystal, the protein can adapt other conformations in solution ranging from fully extended to compact. #1: ![]() Title: Structure of a complete four-domain chitinase from Moritella marina, a marine psychrophilic bacterium Authors: Malecki, P.H. / Raczynska, J.E. / Vorgias, C.E. / Rypniewski, W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 246.9 KB | Display | ![]() |
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PDB format | ![]() | 194.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4mb3C ![]() 4mb5C ![]() 4hmcS 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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | ![]() Mass: 58616.371 Da / Num. of mol.: 1 / Mutation: E153Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose![]() Source method: isolated from a genetically manipulated source |
-Non-polymers , 5 types, 695 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GLY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GLY.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ![]() #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-SO4 / | ![]() #6: Chemical | ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Details
Sequence details | THE SEQUENCE DISCREPANCIES (R452H, A470T) WERE NOT INTENTIONAL MUTATIONS, AND COULD BE THE CORRECT ...THE SEQUENCE DISCREPANC |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.9 % |
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Crystal grow![]() | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02M Na-L-glutamate, 0.02M alanine (racemic), 0.02M glycine, 0.02M lysine HCl (racemic), 0.02M serine (racemic), 0.1M MES/imidazole pH ...Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02M Na-L-glutamate, 0.02M alanine (racemic), 0.02M glycine, 0.02M lysine HCl (racemic), 0.02M serine (racemic), 0.1M MES/imidazole pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Apr 21, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Number: 758690 / Rmerge(I) obs: 0.054 / D res high: 1.48 Å / Num. obs: 110785 / % possible obs: 99.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.48→33.371 Å / Num. all: 110794 / Num. obs: 110794 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 16.83 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 20.52 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.48→1.57 Å / Redundancy: 6.77 % / Rmerge(I) obs: 0.853 / Mean I/σ(I) obs: 2.02 / % possible all: 99.4 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4HMC Resolution: 1.481→33.371 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.14 / σ(F): 1.99 / Phase error: 18.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.49 Å2 / Biso mean: 25.3686 Å2 / Biso min: 10.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.14 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.481→33.371 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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