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Yorodumi- PDB-4fn8: Crystal structure of the Mtb enoyl CoA isomerase (Rv0632c)in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fn8 | ||||||
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Title | Crystal structure of the Mtb enoyl CoA isomerase (Rv0632c)in complex with acetoacetyl CoA | ||||||
Components | Enoyl-CoA hydratase/isomerase family protein | ||||||
Keywords | ISOMERASE / Structural Genomics / TB Structural Genomics Consortium / TBSGC / crotonase superfamily | ||||||
Function / homology | Function and homology information enoyl-CoA hydratase / enoyl-CoA hydratase activity / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.831 Å | ||||||
Authors | Bruning, J.B. / Gao, N. / Hernandez, E.D. / Li, H. / Dang, N. / Hung, L.W. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure and mechanism of the prokaryotic enoyl CoA isomerase (ECI) Authors: Bruning, J.B. / Gao, N. / Hernandez, E.D. / Li, H. / Dang, N. / Hung, L.W. / Moran, S. / Sacchettini, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fn8.cif.gz | 69.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fn8.ent.gz | 48.9 KB | Display | PDB format |
PDBx/mmJSON format | 4fn8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/4fn8 ftp://data.pdbj.org/pub/pdb/validation_reports/fn/4fn8 | HTTPS FTP |
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-Related structure data
Related structure data | 4fn7S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 24466.951 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: echA3, MT0660, Rv0632c / Plasmid: pvp16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P96907, enoyl-CoA hydratase | ||
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#2: Chemical | ChemComp-CAA / | ||
#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: 2.3 Å3/Da / Density % sol: 46.54 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 1.6M ammonium sulfate, 0.1M MES 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 120 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 30, 2009 / Details: osmic mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 7.2 % / Av σ(I) over netI: 42.59 / Number: 151417 / Rmerge(I) obs: 0.06 / Χ2: 2.03 / D res high: 1.83 Å / D res low: 50 Å / Num. obs: 21089 / % possible obs: 99.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.83→50 Å / Num. all: 21089 / Num. obs: 21089 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 17.87 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Χ2: 2.031 / Net I/σ(I): 17.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4FN7 subunit A Resolution: 1.831→25.35 Å / Occupancy max: 1 / Occupancy min: 0.12 / FOM work R set: 0.9014 / SU ML: 0.18 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 15.39 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.986 Å2 / ksol: 0.365 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.6 Å2 / Biso mean: 18.8567 Å2 / Biso min: 5.24 Å2
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Refinement step | Cycle: LAST / Resolution: 1.831→25.35 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %
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