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Yorodumi- PDB-4ggp: Crystal Structure of Selenomethionine containing Trans-2-Enoyl-Co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ggp | ||||||
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Title | Crystal Structure of Selenomethionine containing Trans-2-Enoyl-CoA Reductase from Treponema denticola | ||||||
Components | Trans-2-enoyl-CoA reductase | ||||||
Keywords | OXIDOREDUCTASE / Rossmann Fold / Reductase | ||||||
Function / homology | Function and homology information trans-2-enoyl-CoA reductase (NAD+) / trans-2-enoyl-CoA reductase (NADH) activity / fatty acid biosynthetic process / NAD binding Similarity search - Function | ||||||
Biological species | Treponema denticola (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å | ||||||
Authors | Bond-Watts, B.B. / Weeks, A.M. / Chang, M.C.Y. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Biochemical and Structural Characterization of the trans-Enoyl-CoA Reductase from Treponema denticola. Authors: Bond-Watts, B.B. / Weeks, A.M. / Chang, M.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ggp.cif.gz | 313.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ggp.ent.gz | 265.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ggp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ggp_validation.pdf.gz | 446.6 KB | Display | wwPDB validaton report |
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Full document | 4ggp_full_validation.pdf.gz | 459.2 KB | Display | |
Data in XML | 4ggp_validation.xml.gz | 58.1 KB | Display | |
Data in CIF | 4ggp_validation.cif.gz | 82 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/4ggp ftp://data.pdbj.org/pub/pdb/validation_reports/gg/4ggp | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 44385.316 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Treponema denticola (bacteria) / Strain: ATCC 35405 / Gene: TDE_0597 / Plasmid: pET23a-His10-Tev / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q73Q47, acetoacetyl-CoA reductase #2: 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: 2.48 Å3/Da / Density % sol: 50.3 % |
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Crystal grow | Temperature: 291 K / pH: 7.5 Details: 0.1 M sodium citrate, pH 7.5, 25% PEG 6000, 2.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.979, 0.957 | |||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2011 | |||||||||
Radiation | Monochromator: DOUBLE FLAT CRYSTAL, SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2→20 Å / Num. obs: 114220 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 39.9 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 20.67 | |||||||||
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 4.38 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.05→19.47 Å / SU ML: 0.2 / σ(F): 2 / Phase error: 23.48 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.916 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→19.47 Å
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Refine LS restraints |
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LS refinement shell |
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