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Yorodumi- PDB-4mb3: Crystal structure of E153Q mutant of cold-adapted chitinase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mb3 | ||||||
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Title | Crystal structure of E153Q mutant of cold-adapted chitinase from Moritella marina | ||||||
Components | Chitinase 60 | ||||||
Keywords | HYDROLASE / TIM-barrel / alpha/beta-barrel Ig-like / Immunoglobulin like domain / ChBD / Chitin binding domain / Nag4 / Chitinase / hydrolaze / low activity mutant | ||||||
Function / homology | Function and homology information chitinase / chitinase activity / chitin catabolic process / chitin binding / carbohydrate binding / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Moritella marina (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å | ||||||
Authors | Malecki, P.H. / Vorgias, C.E. / Rypniewski, W. | ||||||
Citation | Journal: Acta Crystallogr D Biol Crystallogr / Year: 2014 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: Journal: Acta Crystallogr.,Sect.D / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mb3.cif.gz | 248.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mb3.ent.gz | 194.6 KB | Display | PDB format |
PDBx/mmJSON format | 4mb3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mb/4mb3 ftp://data.pdbj.org/pub/pdb/validation_reports/mb/4mb3 | HTTPS FTP |
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-Related structure data
Related structure data | 4mb4C 4mb5C 4hmcS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 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.) Moritella marina (bacteria) / Gene: chi60 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / References: UniProt: B1VBB0, chitinase |
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-Non-polymers , 6 types, 878 molecules
#2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-GLY / | #4: Chemical | ChemComp-MPD / ( | #5: Chemical | ChemComp-IMD / | #6: Chemical | ChemComp-CL / | #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.31 % |
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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), 0.02Mserine (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), 0.02Mserine (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: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 0.91841 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Number: 609191 / Rmerge(I) obs: 0.065 / D res high: 1.55 Å / Num. obs: 97957 / % possible obs: 99.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.55→31.44 Å / Num. all: 97965 / Num. obs: 97965 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.55→1.64 Å / Redundancy: 6.18 % / Rmerge(I) obs: 0.878 / Mean I/σ(I) obs: 1.81 / Num. unique all: 15537 / % possible all: 98.7 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HMC Resolution: 1.55→31.44 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8864 / SU ML: 0.15 / σ(F): 1.99 / Phase error: 18.7 / 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: 70.71 Å2 / Biso mean: 26.6212 Å2 / Biso min: 7.85 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.15 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→31.44 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: 30
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