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- PDB-3zm8: Crystal structure of Podospora anserina GH26-CBM35 beta-(1,4)- ma... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zm8 | |||||||||
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Title | Crystal structure of Podospora anserina GH26-CBM35 beta-(1,4)- mannanase | |||||||||
![]() | GH26 ENDO-BETA-1,4-MANNANASE | |||||||||
![]() | HYDROLASE / GLYCOSYL HYDROLASE / CAZY / GH5 | |||||||||
Function / homology | ![]() substituted mannan metabolic process / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / carbohydrate binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Couturier, M. / Roussel, A. / Rosengren, A. / Leone, P. / Stalbrand, H. / Berrin, J.G. | |||||||||
![]() | ![]() Title: Structural and Biochemical Analyses of Glycoside Hydrolase Families 5 and 26 Beta-(1,4)-Mannanases from Podospora Anserina Reveal Differences Upon Manno-Oligosaccharides Catalysis. Authors: Couturier, M. / Roussel, A. / Rosengren, A. / Leone, P. / Stalbrand, H. / Berrin, J.G. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.2 KB | Display | ![]() |
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PDB format | ![]() | 80.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 786.2 KB | Display | ![]() |
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Full document | ![]() | 791.2 KB | Display | |
Data in XML | ![]() | 19.4 KB | Display | |
Data in CIF | ![]() | 27.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zizC ![]() 2bvtS ![]() 2qhaS ![]() 2vx4S ![]() 2whkS 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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Unit cell |
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Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 52848.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: E2GHW2, mannan endo-1,4-beta-mannosidase |
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#2: Polysaccharide | 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 , 4 types, 146 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/HG.gif)
![](data/chem/img/TLA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HG.gif)
![](data/chem/img/TLA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CA / |
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#4: Chemical | ChemComp-HG / |
#5: Chemical | ChemComp-TLA / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 7 Details: 0.1 M TRIS PH 7.0, 0.2 M NACL, 0.8 M POTASSIUM SODIUM TARTRATE, 1 MM HGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 7, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97914 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→50 Å / Num. obs: 18575 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 11.8 % / Biso Wilson estimate: 85.54 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 2.85→3 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 4.6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 2QHA, 2BVT, 2VX4 AND 2WHK Resolution: 2.85→28.3 Å / Cor.coef. Fo:Fc: 0.9267 / Cor.coef. Fo:Fc free: 0.8774 / SU R Cruickshank DPI: 0.58 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.705 / SU Rfree Blow DPI: 0.333 / SU Rfree Cruickshank DPI: 0.327 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CA HG. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=3674. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CA HG. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=3674. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=2.
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Displacement parameters | Biso mean: 68.26 Å2
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Refine analyze | Luzzati coordinate error obs: 0.364 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→28.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→3.02 Å / Total num. of bins used: 9
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