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Yorodumi- PDB-4cd7: The structure of GH113 beta-mannanase AaManA from Alicyclobacillu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cd7 | |||||||||
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Title | The structure of GH113 beta-mannanase AaManA from Alicyclobacillus acidocaldarius in complex with ManIFG and beta-1,4-mannobiose | |||||||||
Components | ENDO-BETA-1,4-MANNANASE | |||||||||
Keywords | HYDROLASE / BETA-MANNOSIDASE / MANNOSIDASE / GLYCOSIDE HYDROLASE / GH26 / GH113 / CAZY / ENZYME-CARBOHYDRATE INTERACTION / GLYCOSIDASE INHIBITION / QUANTUM MECHANICS / BIOCATALYSIS / CONFORMATION | |||||||||
Function / homology | Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / beta-D-mannopyranose / 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / Endo-beta-1,4-mannanase Function and homology information | |||||||||
Biological species | ALICYCLOBACILLUS ACIDOCALDARIUS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | |||||||||
Authors | Williams, R.J. / Iglesias-Fernandez, J. / Stepper, J. / Jackson, A. / Thompson, A.J. / Lowe, E.C. / White, J.M. / Gilbert, H.J. / Rovira, C. / Davies, G.J. / Williams, S.J. | |||||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014 Title: Combined Inhibitor Free-Energy Landscape and Structural Analysis Reports on the Mannosidase Conformational Coordinate. Authors: Williams, R.J. / Iglesias-Fernandez, J. / Stepper, J. / Jackson, A. / Thompson, A.J. / Lowe, E.C. / White, J.M. / Gilbert, H.J. / Rovira, C. / Davies, G.J. / Williams, S.J. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" 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. THE SHEETS PRESENTED AS "BA" 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cd7.cif.gz | 280.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cd7.ent.gz | 227 KB | Display | PDB format |
PDBx/mmJSON format | 4cd7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cd7_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4cd7_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4cd7_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 4cd7_validation.cif.gz | 42.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/4cd7 ftp://data.pdbj.org/pub/pdb/validation_reports/cd/4cd7 | HTTPS FTP |
-Related structure data
Related structure data | 4cd4C 4cd5C 4cd6C 4cd8C 3civS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36342.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ALICYCLOBACILLUS ACIDOCALDARIUS (bacteria) Strain: TC-12-31 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: A5H1I6, mannan endo-1,4-beta-mannosidase #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Sugar | #5: Water | ChemComp-HOH / | |
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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: 2.52 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | pH: 4.6 / Details: 0.1 M SODIUM ACETATE PH 4.6, 4% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 26, 2013 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→76.59 Å / Num. obs: 88667 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.8 / % possible all: 78.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CIV Resolution: 1.65→70.11 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.143 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.621 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→70.11 Å
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Refine LS restraints |
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