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- PDB-4bpz: Crystal structure of lamA_E269S from Zobellia galactanivorans in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bpz | |||||||||
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Title | Crystal structure of lamA_E269S from Zobellia galactanivorans in complex with a trisaccharide of 1,3-1,4-beta-D-glucan. | |||||||||
![]() | ENDO-1,3-BETA-GLUCANASE, FAMILY GH16 | |||||||||
![]() | HYDROLASE / MARINE LAMINARINASE | |||||||||
Function / homology | ![]() glucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity / carbohydrate metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Labourel, A. / Jam, M. / Jeudy, A. / Czjzek, M. / Michel, G. | |||||||||
![]() | ![]() Title: The Beta-Glucanase Zglama from Zobellia Galactanivorans Evolved a Bent Active Site Adapted for Efficient Degradation of Algal Laminarin. Authors: Labourel, A. / Jam, M. / Jeudy, A. / Hehemann, J.H. / Czjzek, M. / Michel, G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 250.4 KB | Display | ![]() |
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PDB format | ![]() | 200.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 985.6 KB | Display | ![]() |
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Full document | ![]() | 998.9 KB | Display | |
Data in XML | ![]() | 28.3 KB | Display | |
Data in CIF | ![]() | 42.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bowC ![]() 4bq1SC C: citing same article ( S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 29219.875 Da / Num. of mol.: 2 / Fragment: RESIDUES 136-383 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) AND INHOUSE AT ROSCOFF COLLECTION Production host: ![]() ![]() References: UniProt: G0L5X4, glucan endo-1,3-beta-D-glucosidase #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCTION CONTAINS THE CATALYTIC MODULE ONLY. THE N- TERMINAL PKD-MODULE HAS NOT BEEN CLONED. ...THE CONSTRUCTI | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.93 % / Description: NONE |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 4 Details: MONO-CRYSTALS OF LAMAE269S IN COMPLEX WITH MLG TRISACCHARIDES WERE OBTAINED AS FOLLOWED: 2 MICROL OF THE MIXTURE ENZYME/OLIGOSACCHARIDES (11,7 MG.ML-1 OF ENZYME, 0,04% (W/V) OF MLG ...Details: MONO-CRYSTALS OF LAMAE269S IN COMPLEX WITH MLG TRISACCHARIDES WERE OBTAINED AS FOLLOWED: 2 MICROL OF THE MIXTURE ENZYME/OLIGOSACCHARIDES (11,7 MG.ML-1 OF ENZYME, 0,04% (W/V) OF MLG DEGRADATION PRODUCTS) WERE ADDED TO 1 MICROL OF RESERVOIR SOLUTION CONTAINING 100 MM MIB BUFFER PH4.0, 17% OF PEG 1500 AND 10% OF GLYCEROL IN HANGING DROPS AT 12 CELSIUS DEGREE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→47.56 Å / Num. obs: 181382 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.13→1.19 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.9 / % possible all: 95.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4BQ1 Resolution: 1.13→71.34 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.235 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN IN THE INPUT. U VALUES WITH TLS ADDED
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.351 Å2
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Refinement step | Cycle: LAST / Resolution: 1.13→71.34 Å
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Refine LS restraints |
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