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Yorodumi- PDB-4mi2: Crystal structure of putative Enoyl-CoA hydratase/isomerase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mi2 | ||||||
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Title | Crystal structure of putative Enoyl-CoA hydratase/isomerase from Mycobacterium abscessus | ||||||
Components | Putative enoyl-CoA hydratase/isomerase | ||||||
Keywords | ISOMERASE / SSGCID / NIH / NIAID / SBRI / EMERALD BIO / PHENYLACETATE DEGRADATION / PHENYLETHYLAMINE DEGRADATION / Structural Genomics / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium abscessus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of putative Enoyl-CoA hydratase/isomerase from Mycobacterium abscessus Authors: Davies, D.R. / Lukacs, C. / Lorimer, D. / Edwards, T.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mi2.cif.gz | 279.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mi2.ent.gz | 229.4 KB | Display | PDB format |
PDBx/mmJSON format | 4mi2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/4mi2 ftp://data.pdbj.org/pub/pdb/validation_reports/mi/4mi2 | 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 | THE ASYMMETRIC UNIT IS THE SAME AS THE BIOLOGICAL ASSEMBLY |
-Components
#1: Protein | Mass: 27367.086 Da / Num. of mol.: 3 / Fragment: PUTATIVE ENOYL-COA HYDRATASE/ISOMERASE Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: ATCC 19977 / Gene: MAB_0905 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: B1MJ43, 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase #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: 2.68 Å3/Da / Density % sol: 54.1 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: EBS INTERNAL TRACKING NUMBER 500 MM NACL, 2 MM DTT, 0.025% SODIUM AZIDE, 5% GLYCEROL, 0.4 UL X 0.4 UL DROP WITH MORPHEUS SCREEN CONDITION E12: 0.12 M DI -ETHYLENEGLYCOL; TRI-ETHYLENEGLYCOL, ...Details: EBS INTERNAL TRACKING NUMBER 500 MM NACL, 2 MM DTT, 0.025% SODIUM AZIDE, 5% GLYCEROL, 0.4 UL X 0.4 UL DROP WITH MORPHEUS SCREEN CONDITION E12: 0.12 M DI -ETHYLENEGLYCOL; TRI-ETHYLENEGLYCOL, TETRA-ETHYLENEGLYCOL AND PENTA-ETHYLENEGLYCOL, 0.1 M BUFFER SYSTEM 3 (TRIS BASE, BICINE, PH 8.5), 37.5% MPD/PEG 1000/ PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97625, 0.9774 | |||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 1, 2012 | |||||||||
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Highest resolution: 2.3 Å / Num. obs: 40335 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.93 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 15.31 | |||||||||
Reflection shell | Resolution: 2.3→2.36 Å / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 4.2 / % possible all: 99.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→47.51 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.924 / SU B: 10.107 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.262 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
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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: 23.79 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→47.51 Å
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