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Yorodumi- PDB-2pgn: The crystal structure of FAD and ThDP-dependent Cyclohexane-1,2-d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pgn | ||||||
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Title | The crystal structure of FAD and ThDP-dependent Cyclohexane-1,2-dione Hydrolase in Complex with Cyclohexane-1,2-dione | ||||||
Components | Cyclohexane-1,2-dione Hydrolase (Cdh) | ||||||
Keywords | HYDROLASE / Three alpha/beta domains | ||||||
Function / homology | Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / CYCLOHEXANE-1,2-DIONE / FLAVIN-ADENINE DINUCLEOTIDE / THIAMINE DIPHOSPHATE Function and homology information | ||||||
Biological species | Azoarcus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / known crystal structure / Resolution: 1.2 Å | ||||||
Authors | Fraas, S. / Warkentin, E. / Ermler, U. | ||||||
Citation | Journal: To be Published Title: The crystal structure of FAD and ThDP-dependent Cyclohexane-1,2-dione Hydrolase in Complex with Cyclohexane-1,2-dione Authors: Fraas, S. / Steinbach, A.K. / Warkentin, E. / Kroneck, P.M.H. / Ermler, U. | ||||||
History |
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Remark 999 | sequence The sequence is not available in UniProt database at the time of processing. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pgn.cif.gz | 480.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pgn.ent.gz | 388.8 KB | Display | PDB format |
PDBx/mmJSON format | 2pgn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/2pgn ftp://data.pdbj.org/pub/pdb/validation_reports/pg/2pgn | HTTPS FTP |
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-Related structure data
Related structure data | |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 63362.930 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azoarcus sp. (bacteria) / Strain: 22Lin |
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-Non-polymers , 6 types, 1285 molecules
#2: Chemical | #3: Chemical | ChemComp-P6G / #4: Chemical | #5: Chemical | #6: Chemical | #7: 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: 2.18 Å3/Da / Density % sol: 43.48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 23% PEG 400, 0.01M sodium acetate, 3mM HEPES, 0.5mM ThDP, 0.5mM NAD, 0.1M NaCl. Crystal soaked in 47% PEG 400, 0.02M sodium acetate, 5mM 1,2 cyclohexanedione, pH 7.0, VAPOR DIFFUSION, ...Details: 23% PEG 400, 0.01M sodium acetate, 3mM HEPES, 0.5mM ThDP, 0.5mM NAD, 0.1M NaCl. Crystal soaked in 47% PEG 400, 0.02M sodium acetate, 5mM 1,2 cyclohexanedione, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 3, 2005 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→40 Å / Num. all: 388867 / Num. obs: 379045 / % possible obs: 84.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 12.26 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 13.58 |
Reflection shell | Resolution: 1.1→1.2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.7 / Num. measured obs: 187829 / Num. unique all: 50802 / % possible all: 49.9 |
-Processing
Software |
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Refinement | Method to determine structure: known crystal structure / Resolution: 1.2→10 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.52 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 12.78 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Total num. of bins used: 20
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