+Open data
-Basic information
Entry | Database: PDB / ID: 5eep | ||||||
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Title | Crystal structure of E. coli CsdE | ||||||
Components | CsdA-binding activator | ||||||
Keywords | LIGASE / sulfur-accepting protein / SufE superfamily / CsdA interaction / sulfur utilization | ||||||
Function / homology | Function and homology information cyclic threonylcarbamoyladenosine biosynthetic process / sulfur carrier activity Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å | ||||||
Authors | Park, S.Y. | ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2016 Title: The crystal structure of Escherichia coli CsdE Authors: Kenne, A.N. / Kim, S. / Park, S.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eep.cif.gz | 69.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eep.ent.gz | 50.6 KB | Display | PDB format |
PDBx/mmJSON format | 5eep.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/5eep ftp://data.pdbj.org/pub/pdb/validation_reports/ee/5eep | 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16208.464 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ECONIH1_16050, SK78_01951 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A1ADS4, UniProt: P0AGF2*PLUS |
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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: 2.12 Å3/Da / Density % sol: 42.06 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30% (w/v) PEG 4000, 0.2M sodium acetate, 0.1M Tris, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 5950 / % possible obs: 99.8 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 55.4 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 10.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 2.4→41.69 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.912 / SU B: 25.559 / SU ML: 0.29 / Cross valid method: THROUGHOUT / ESU R: 0.513 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 39.757 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→41.69 Å
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Refine LS restraints |
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