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Yorodumi- PDB-3dxp: Crystal structure of a putative aminoglycoside phosphotransferase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dxp | ||||||
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Title | Crystal structure of a putative aminoglycoside phosphotransferase (reut_a1007) from ralstonia eutropha jmp134 at 2.32 A resolution | ||||||
Components | putative acyl-CoA dehydrogenase | ||||||
Keywords | TRANSFERASE / Protein kinase-like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Ralstonia eutropha JMP134 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.32 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of putative acyl-CoA dehydrogenase (YP_295230.1) from RALSTONIA EUTROPHA JMP134 at 2.32 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dxp.cif.gz | 79.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dxp.ent.gz | 61.8 KB | Display | PDB format |
PDBx/mmJSON format | 3dxp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/3dxp ftp://data.pdbj.org/pub/pdb/validation_reports/dx/3dxp | 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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Details | THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE PROTOMER MAY FORM A DIMER BASED ON CRYSTAL PACKING ANALYSIS. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). |
-Components
#1: Protein | Mass: 41197.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ralstonia eutropha JMP134 (bacteria) / Gene: YP_295230.1, Reut_A1007 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q473P7 |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-EDO / |
#5: Water | ChemComp-HOH / |
Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.17 Details: 20.0% polyethylene glycol 8000, 0.3M calcium acetate, 0.1M MES pH 6.17, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97971,0.97956 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 26, 2008 / Details: Flat collimating mirror, toroid focusing mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.32→28.989 Å / Num. obs: 18395 / % possible obs: 99.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 33.49 Å2 / Rmerge(I) obs: 0.129 / Rsym value: 0.129 / Net I/σ(I): 5.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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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: 2.32→28.989 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.895 / SU B: 11.451 / SU ML: 0.254 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.39 / ESU R Free: 0.28 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION 3. CALCIUM, ACETATE AND 1,2-ETHANEDIOL WERE MODELED BASED ON CRYSTALLIZATION AND CRYOPROTECTION CONDITIONS. 4. DUE TO A STRONG ICE RING, 991 REFLECTIONS BETWEEN 2.656-2.586 ANGSTROMS WERE OMITTED FROM THE FINAL REFINEMENT. 5. THERE ARE TWO REGIONS OF UNMODELED DENSITY IN THE SOLVENT STRUCTURE NEAR AMINO ACIDS A90 AND A94. 6. RESIDUES A267 AND A268 ARE RAMACHANDRAN OUTLIERS IN A REGION WHERE THE ELECTRON DENSITY IS DIFFICULT TO INTERPRET.
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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: 37.949 Å2
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Refinement step | Cycle: LAST / Resolution: 2.32→28.989 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.32→2.38 Å / Total num. of bins used: 20
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