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Yorodumi- PDB-2oyo: Crystal structure of Uncharacterized peroxidase-related protein (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oyo | ||||||
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Title | Crystal structure of Uncharacterized peroxidase-related protein (YP_604910.1) from Deinococcus geothermalis DSM 11300 at 1.51 A resolution | ||||||
Components | Uncharacterized peroxidase-related protein | ||||||
Keywords | OXIDOREDUCTASE / YP_604910.1 / Uncharacterised peroxidase-related / Uncharacterized peroxidase-related / Carboxymuconolactone decarboxylase family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Deinococcus geothermalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.51 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Uncharacterized peroxidase-related protein (YP_604910.1) from Deinococcus geothermalis DSM 11300 at 1.51 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 | 2oyo.cif.gz | 91.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oyo.ent.gz | 73.3 KB | Display | PDB format |
PDBx/mmJSON format | 2oyo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/2oyo ftp://data.pdbj.org/pub/pdb/validation_reports/oy/2oyo | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 21912.307 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus geothermalis (bacteria) / Strain: DSM 11300 / Gene: YP_604910.1, Dgeo_1446 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q1IYE3 #2: Chemical | #3: 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: 2.38 Å3/Da / Density % sol: 48.41 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 Details: NANODROP, 40.0% MPD, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97916, 0.97886 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 7, 2007 / Details: Flat mirror (vertical focusing) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.51→39.163 Å / Num. obs: 64521 / % possible obs: 96.5 % / Biso Wilson estimate: 17.262 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 9.57 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.51→39.163 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.97 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.078 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. THE 2-METHYL-2,4-PENTANEDIOL MOLECULES FROM THE CRYSTALLIZATION WERE MODELED INTO THE STRUCTURE. 4. UNEXPLAINED ELECTRON DENSITIES OBSERVED NEAR RESIDUES 189 AND 192 OF THE B SUBUNIT 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.894 Å2
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Refinement step | Cycle: LAST / Resolution: 1.51→39.163 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.51→1.549 Å / Total num. of bins used: 20
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