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Yorodumi- PDB-2b20: Crystal Structure of Enterochelin Esterase from Shigella flexneri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2b20 | ||||||
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Title | Crystal Structure of Enterochelin Esterase from Shigella flexneri Enterochelin Esterase | ||||||
Components | enterochelin esterase | ||||||
Keywords | TRANSPORT PROTEIN / alpha-beta-alpha-sandwich / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information enterochelin esterase activity / carboxylic ester hydrolase activity / iron ion transport / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Shigella flexneri 2a str. 2457T (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.95 Å | ||||||
Authors | Kim, Y. / Maltseva, N. / Dementieva, I. / Quartey, P. / Holzle, D. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Enterochelin Esterase from Shigella flexneri Enterochelin Esterase Authors: Kim, Y. / Maltseva, N. / Dementieva, I. / Quartey, P. / Holzle, D. / Collart, F. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b20.cif.gz | 90 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b20.ent.gz | 72.6 KB | Display | PDB format |
PDBx/mmJSON format | 2b20.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/2b20 ftp://data.pdbj.org/pub/pdb/validation_reports/b2/2b20 | 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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-Components
#1: Protein | Mass: 46304.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri 2a str. 2457T (bacteria) Species: Shigella flexneri / Strain: 2a str. 2457T / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q83SB9, UniProt: A0A0H2VTI6*PLUS |
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#2: Chemical | ChemComp-TLA / |
#3: 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: 3.1 Å3/Da / Density % sol: 60.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: potassium/sodium tartrate, CHES, litium sulfate, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 11, 2005 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→50 Å / Num. all: 13375 / Num. obs: 12690 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.95→3.06 Å / Redundancy: 16.6 % / Rmerge(I) obs: 0.969 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1198 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.95→40.11 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.899 / SU B: 39.97 / SU ML: 0.348 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.436 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 81.509 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→40.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.026 Å / Total num. of bins used: 20
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