+Open data
-Basic information
Entry | Database: PDB / ID: 3ziz | ||||||
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Title | Crystal structure of Podospora anserina GH5 beta-(1,4)-mannanase | ||||||
Components | GH5 ENDO-BETA-1,4-MANNANASE | ||||||
Keywords | HYDROLASE / MANNANASE / GLYCOSYL HYDROLASE / CAZY | ||||||
Function / homology | Function and homology information mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | PODOSPORA ANSERINA (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Couturier, M. / Roussel, A. / Rosengren, A. / Leone, P. / Stalbrand, H. / Berrin, J.G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ziz.cif.gz | 93.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ziz.ent.gz | 68.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ziz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ziz_validation.pdf.gz | 438.8 KB | Display | wwPDB validaton report |
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Full document | 3ziz_full_validation.pdf.gz | 438.8 KB | Display | |
Data in XML | 3ziz_validation.xml.gz | 18 KB | Display | |
Data in CIF | 3ziz_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/3ziz ftp://data.pdbj.org/pub/pdb/validation_reports/zi/3ziz | HTTPS FTP |
-Related structure data
Related structure data | 3zm8C 1qnoS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42496.988 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PODOSPORA ANSERINA (fungus) / Strain: S MAT / Plasmid: PPICZAA / Production host: PICHIA PASTORIS (fungus) / Strain (production host): X33 References: UniProt: E2GHW1, UniProt: B2B3C0*PLUS, mannan endo-1,4-beta-mannosidase |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-TRS / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: 8.5 Details: TRIS 0.1M PH 8.5, 0.2 M SODIUM ACETATE, 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97914 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97914 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. obs: 62519 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 8.4 % / Biso Wilson estimate: 10.99 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.4 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QNO Resolution: 1.4→28.95 Å / Cor.coef. Fo:Fc: 0.9657 / Cor.coef. Fo:Fc free: 0.9576 / SU R Cruickshank DPI: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.057 / SU Rfree Blow DPI: 0.057 / SU Rfree Cruickshank DPI: 0.055 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=3118. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=3118. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=75.
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Displacement parameters | Biso mean: 13.05 Å2
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Refine analyze | Luzzati coordinate error obs: 0.126 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→28.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.44 Å / Total num. of bins used: 20
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