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Yorodumi- PDB-2o2g: Crystal structure of Dienelactone hydrolase (YP_324580.1) from An... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2o2g | ||||||
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Title | Crystal structure of Dienelactone hydrolase (YP_324580.1) from Anabaena variabilis ATCC 29413 at 1.92 A resolution | ||||||
Components | Dienelactone hydrolase | ||||||
Keywords | HYDROLASE / YP_324580.1 / Dienelactone hydrolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Dienelactone hydrolase / Dienelactone hydrolase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / hydrolase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Dienelactone hydrolase Function and homology information | ||||||
Biological species | Anabaena variabilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.92 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Dienelactone hydrolase (YP_324580.1) from Anabaena variabilis ATCC 29413 at 1.92 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Remark 999 | SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o2g.cif.gz | 56.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o2g.ent.gz | 42.6 KB | Display | PDB format |
PDBx/mmJSON format | 2o2g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/2o2g ftp://data.pdbj.org/pub/pdb/validation_reports/o2/2o2g | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24214.088 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anabaena variabilis (bacteria) / Gene: YP_324580.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3M5Q1 | ||||
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#2: Chemical | #3: Chemical | #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: 2.1 Å3/Da / Density % sol: 41.41 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 9.5 Details: 1.26M (NH4)2SO4, 0.2M NaCl, 0.1M CHES pH 9.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.94645, 0.97942, 0.97921 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 19, 2006 / Details: Adjustable focusing mirrors in K-B geometry | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) Double Crystal Monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.92→39.163 Å / Num. obs: 14877 / % possible obs: 92 % / Redundancy: 3.9 % / Biso Wilson estimate: 20.056 Å2 / Rmerge(I) obs: 0.07 / Χ2: 1.068 / Net I/σ(I): 9.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.92→39.163 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.103 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.172 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.70 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. TWO SULFATE MOLECULES FROM CRYSTALLIZATION SOLUTION AND TWO ETHYLENE GLYCOL MOLECULES (CRYOPROTECTANT) ARE INCLUDED IN THE MODEL. 5. ELECTRON DENSITY CORRESPONDING TO RESIDUES 1-6 WAS DISORDERED AND THESE RESIDUES WERE NOT MODELED.
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.006 Å2
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Refinement step | Cycle: LAST / Resolution: 1.92→39.163 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.92→1.969 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 32.1491 Å / Origin y: 4.2548 Å / Origin z: 15.1916 Å
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Refinement TLS group | Selection: ALL |