+Open data
-Basic information
Entry | Database: PDB / ID: 5c22 | ||||||
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Title | Crystal structure of Zn-bound HlyD from E. coli | ||||||
Components | Chromosomal hemolysin D | ||||||
Keywords | PROTEIN TRANSPORT / HlyD / type I secretion system / Zn SAD / multicrystal averaging | ||||||
Function / homology | Function and homology information protein secretion by the type I secretion system / protein secretion / killing of cells of another organism / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.302 Å | ||||||
Authors | Ha, N.C. / Kim, J.S. | ||||||
Citation | Journal: Structure / Year: 2016 Title: Crystal Structure of a Soluble Fragment of the Membrane Fusion Protein HlyD in a Type I Secretion System of Gram-Negative Bacteria Authors: Kim, J.S. / Song, S. / Lee, M. / Lee, S. / Lee, K. / Ha, N.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c22.cif.gz | 223.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c22.ent.gz | 180 KB | Display | PDB format |
PDBx/mmJSON format | 5c22.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5c22_validation.pdf.gz | 462.6 KB | Display | wwPDB validaton report |
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Full document | 5c22_full_validation.pdf.gz | 471.4 KB | Display | |
Data in XML | 5c22_validation.xml.gz | 37.2 KB | Display | |
Data in CIF | 5c22_validation.cif.gz | 51.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/5c22 ftp://data.pdbj.org/pub/pdb/validation_reports/c2/5c22 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 32226.791 Da / Num. of mol.: 4 / Fragment: UNP residues 57-333 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hlyD / Production host: Escherichia coli (E. coli) / References: UniProt: O87505, UniProt: P09986*PLUS #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.23 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Sodium cacodylate trihydrate, 0.2M Calcium acetate, 14% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.28245 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28245 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→37.2 Å / Num. obs: 118968 / % possible obs: 100 % / Redundancy: 65.8 % / Net I/σ(I): 21.6 |
-Processing
Software |
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Refinement | Resolution: 2.302→37.2 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 28.73 / Stereochemistry target values: ML Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.302→37.2 Å
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Refine LS restraints |
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LS refinement shell |
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