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Yorodumi- PDB-1h3g: Cyclomaltodextrinase from Flavobacterium sp. No. 92: from DNA seq... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h3g | ||||||
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Title | Cyclomaltodextrinase from Flavobacterium sp. No. 92: from DNA sequence to protein structure | ||||||
Components | Cyclomaltodextrinase | ||||||
Keywords | HYDROLASE / CYCLOMALTODEXTRINASE / GLYCOSIDASE | ||||||
Function / homology | Function and homology information cyclomaltodextrinase / cyclomaltodextrinase activity / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Flavobacterium sp. 92 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Fritzsche, H.B. / Schwede, T. / Jelakovic, S. / Schulz, G.E. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 2003 Title: Covalent and Three-Dimensional Structure of the Cyclodextrinase from Flavobacterium Sp. No. 92. Authors: Fritzsche, H.B. / Schwede, T. / Schulz, G.E. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h3g.cif.gz | 255.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h3g.ent.gz | 216.6 KB | Display | PDB format |
PDBx/mmJSON format | 1h3g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/1h3g ftp://data.pdbj.org/pub/pdb/validation_reports/h3/1h3g | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-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: (Code: given Matrix: (0.450916, 0.849463, -0.274019), Vector: |
-Components
#1: Protein | Mass: 69259.969 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Flavobacterium sp. 92 (bacteria) / Gene: cdase / Plasmid: PET22B+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8KKG0, cyclomaltodextrinase #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | Compound details | DEGRADATION OF CYCLODEXTRINS AND LINEAR MALTOOLIGOSACCHARIDES, HYDROLIZATION OF DIFFERENT ...DEGRADATIO | |
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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: 2.74 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.50 | ||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9393 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 3, 2001 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL FOCUSSING / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→21 Å / Num. obs: 86572 / % possible obs: 99.9 % / Observed criterion σ(I): 1.8 / Redundancy: 7.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9 |
Reflection | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 25 Å / Redundancy: 7.3 % / Num. measured all: 629678 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS Highest resolution: 2.08 Å / % possible obs: 99.9 % / Redundancy: 7.3 % / Num. unique obs: 8625 / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→21.1 Å / SU B: 6.4 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.17 Details: FIRST CNS WAS USED FOR REFINEMENT FOLLOWED BY TLS REFINEMENT IN REFMAC
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Displacement parameters | Biso mean: 27.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→21.1 Å
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Refinement | *PLUS Lowest resolution: 21 Å / Num. reflection obs: 78164 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.08 Å / Lowest resolution: 2.13 Å / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.219 / Num. reflection obs: 4817 |