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Yorodumi- PDB-2fwm: Crystal Structure of E. coli EntA, a 2,3-dihydrodihydroxy benzoat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fwm | ||||||
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Title | Crystal Structure of E. coli EntA, a 2,3-dihydrodihydroxy benzoate dehydrogenase | ||||||
Components | 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / enterobactin / Rossmann Fold / chorismate metabolism / short-chain oxidoreductase / tetramer | ||||||
Function / homology | Function and homology information 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase / 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase activity / enterobactin biosynthetic process / protein-containing complex / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Gulick, A.M. / Duax, W.L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2006 Title: Determination of the crystal structure of EntA, a 2,3-dihydro-2,3-dihydroxybenzoic acid dehydrogenase from Escherichia coli. Authors: Sundlov, J.A. / Garringer, J.A. / Carney, J.M. / Reger, A.S. / Drake, E.J. / Duax, W.L. / Gulick, A.M. | ||||||
History |
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Remark 999 | SEQUENCE After removal of the tag with TEV protease, a Gly-His sequence remains upstream of Met at position 1 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fwm.cif.gz | 53.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fwm.ent.gz | 38.2 KB | Display | PDB format |
PDBx/mmJSON format | 2fwm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/2fwm ftp://data.pdbj.org/pub/pdb/validation_reports/fw/2fwm | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Tetramer formed around crystallographic 222 symmetry |
-Components
#1: Protein | Mass: 26466.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 / Gene: entA / Plasmid: pET15b-TEV / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P15047, 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase |
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#2: 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: 2.02 Å3/Da / Density % sol: 39.2 % |
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Crystal grow | Temperature: 277 K / pH: 5 Details: 2% PEG4000, 2% ethylene glycol, 300 mM AmSO4, 50 mM NaSuccinate, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 5.00 |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9793 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 2, 2005 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 14485 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.059 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.298 / % possible all: 70 |
-Phasing
Phasing | Method: MAD | |||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing dm | FOM : 0.86 / FOM acentric: 0.86 / FOM centric: 0.83 / Reflection: 14387 / Reflection acentric: 12756 / Reflection centric: 1631 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.454 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.154 / Stereochemistry target values: Engh & Huber
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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: 21.48 Å2
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Refinement step | Cycle: LAST / Resolution: 2→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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