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- PDB-4bow: Crystal structure of LamA_E269S from Z. galactanivorans in comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bow | |||||||||
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Title | Crystal structure of LamA_E269S from Z. galactanivorans in complex with laminaritriose and laminaritetraose | |||||||||
![]() | ENDO-1,3-BETA-GLUCANASE, FAMILY GH16 | |||||||||
![]() | HYDROLASE / MARINE LAMINARINASE / FAMILY GH16 GLYCOSIDE HYDROLASE | |||||||||
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. / 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 | ![]() | 247.2 KB | Display | ![]() |
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PDB format | ![]() | 197.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 780.1 KB | Display | ![]() |
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Full document | ![]() | 790.6 KB | Display | |
Data in XML | ![]() | 27.8 KB | Display | |
Data in CIF | ![]() | 41.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bpzC ![]() 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29219.875 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 136-383 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) AND IN HOUSE AT ROSCOFF COLLECTION Production host: ![]() ![]() References: UniProt: G0L5X4, glucan endo-1,3-beta-D-glucosidase |
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-Sugars , 3 types, 3 molecules ![](data/chem/img/BGC.gif)
#2: Polysaccharide | beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#6: Sugar | ChemComp-BGC / |
-Non-polymers , 3 types, 548 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-NA / | #7: Water | ChemComp-HOH / | |
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-Details
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: 52 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 100 MM MIB PH 4.0, 19% PEG1500, HANGING DROP AT 20 DEGREES CELSIUS MIXING 2 MICROL OF PROTEIN (13.7 MG/ML SUPPLEMENTED WITH 5 MM PURIFIED LAMINARIHEXAOSE) WITH 1 MICROL OF RESERVOIR SOLUTION |
-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: 1.35→40.44 Å / Num. obs: 107451 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.35→1.42 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.3 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4BQ1 Resolution: 1.35→67.44 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.88 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT 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: 23.543 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→67.44 Å
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Refine LS restraints |
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