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Yorodumi- PDB-2pgo: The crystal structure of FAD and ThDP dependent Cyclohexane-1,2-d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pgo | ||||||
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Title | The crystal structure of FAD and ThDP dependent Cyclohexane-1,2-dione Hydrolase (Cdh) from Azoarcus sp. strain 22Lin | ||||||
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 / FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / THIAMINE DIPHOSPHATE Function and homology information | ||||||
Biological species | Azoarcus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD, MIRAS / Resolution: 1.26 Å | ||||||
Authors | Steinbach, A.K. / Warkentin, E. / Kroneck, P.M.H. / Ermler, U. | ||||||
Citation | Journal: To be Published Title: The crystal structure of FAD and ThDP dependent Cyclohexane-1,2-dione Hydrolase (Cdh) from Azoarcus sp. strain 22Lin Authors: Steinbach, A.K. / Harder, J. / 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 | 2pgo.cif.gz | 470.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pgo.ent.gz | 379.9 KB | Display | PDB format |
PDBx/mmJSON format | 2pgo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/2pgo ftp://data.pdbj.org/pub/pdb/validation_reports/pg/2pgo | 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 , 7 types, 1223 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-PO4 / | #8: 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: 2.17 Å3/Da / Density % sol: 43.41 % Description: the structure was solved by combined SAD and MIR. Anomalous data were collected at 1.005 A for a crystal soaked with mercuric acetate (up to 2.5A res.) and at 1.072 A for a K2PtCl6 ...Description: the structure was solved by combined SAD and MIR. Anomalous data were collected at 1.005 A for a crystal soaked with mercuric acetate (up to 2.5A res.) and at 1.072 A for a K2PtCl6 soaked crystal (up to 2.8A res.) both at ESRF ID14-4. Further data were colleted in-house (Cu-Ka) for a 'Pip' and a 'Terpy' heavy atom derivative, respectively, both up to 2.7 A resolution. The deposited coordinates are from high resolution data collected a 0.939A. |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 60% MPD, 0.02M sodium acetate, 0.2M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 9, 2003 | ||||||||||||||||||||||||||||||
Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.2→40 Å / Num. obs: 259345 / % possible obs: 77 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.48 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 12 | ||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.2→1.3 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.115 / Mean I/σ(I) obs: 5.1 / Num. unique all: 20256 / % possible all: 14 |
-Processing
Software |
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Refinement | Method to determine structure: MAD, MIRAS / Resolution: 1.26→5 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.736 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.031 / ESU R Free: 0.032 / 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: 8.189 Å2
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Refinement step | Cycle: LAST / Resolution: 1.26→5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.26→1.291 Å / Total num. of bins used: 20
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