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- PDB-3c8d: Crystal structure of the enterobactin esterase FES from Shigella ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3c8d | ||||||
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Title | Crystal structure of the enterobactin esterase FES from Shigella flexneri in the presence of 2,3-Di-hydroxy-N-benzoyl-glycine | ||||||
![]() | Enterochelin esterase | ||||||
![]() | HYDROLASE / alpha-beta-alpha sandwich / IroD / Iron aquisition / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | ![]() enterochelin esterase activity / carboxylic ester hydrolase activity / iron ion transport / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, Y. / Maltseva, N. / Abergel, R. / Holzle, D. / Raymond, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: Siderophore Mediated Iron Acquisition: Structure and Specificity of Enterobactin Esterase from Shigella flexneri. Authors: Kim, Y. / Maltseva, N. / Abergel, R. / Holzle, D. / Raymond, K. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 634 KB | Display | ![]() |
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PDB format | ![]() | 522.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 496.1 KB | Display | ![]() |
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Full document | ![]() | 544 KB | Display | |
Data in XML | ![]() | 73.4 KB | Display | |
Data in CIF | ![]() | 104 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3c87C ![]() 3c8hC ![]() 2b20S S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 45928.922 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species: Shigella flexneri / Strain: 2457T / Serotype 2a / Gene: fes, S0503, SF0497 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: ![]() ![]() #2: Chemical | ChemComp-CIT / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20% PEG 3000, 0.1 M Citrate pH 5.5, 3 mM DHBG, 1 mM FeCl3, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 8, 2006 / Details: Mirrors |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection twin | Type: merohedral / Operator: h,-k,-l / Fraction: 0.354 |
Reflection | Resolution: 1.8→48.48 Å / Num. all: 149451 / Num. obs: 149451 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 26.65 Å2 / Rsym value: 0.062 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.8→1.81 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.39 / Num. unique all: 13227 / Rsym value: 0.379 / % possible all: 86.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2B20 Resolution: 1.8→48.48 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: 1. TWINNING: TWIN LAW: h,-k,-l, TWIN FRACTION: 0.354. 2. When refining TLS, the output PDB file always has the ANISOU records for the atoms involved in TLS groups. The anisotropic B-factor ...Details: 1. TWINNING: TWIN LAW: h,-k,-l, TWIN FRACTION: 0.354. 2. When refining TLS, the output PDB file always has the ANISOU records for the atoms involved in TLS groups. The anisotropic B-factor in ANISOU records is the total B-factor (B_tls + B_individual). The isotropic equivalent B-factor in ATOM records is the mean of the trace of the ANISOU matrix divided by 10000 and multiplied by 8*pi^2 and represents the isotropic equivalent of the total B-factor (B_tls + B_individual). To obtain the individual B-factors, one needs to compute the TLS component (B_tls) using the TLS records in the PDB file header and then subtract it from the total B-factors (on the ANISOU records).
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Solvent computation | Bsol: 42.52 Å2 / ksol: 0.35 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.09 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→48.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.83 Å / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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