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Yorodumi- PDB-4aeq: Crystal structure of the dimeric immunity protein Cmi solved by d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4aeq | ||||||
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Title | Crystal structure of the dimeric immunity protein Cmi solved by direct methods (Arcimboldo) | ||||||
Components | COLICIN-M IMMUNITY PROTEIN | ||||||
Keywords | IMMUNE SYSTEM / 3D DOMAIN SWAP | ||||||
Function / homology | YebF/Cmi domain profile. / YebF/Colicin-M immunity protein / YebF/Cmi superfamily / YebF-like protein / bacteriocin immunity / PHOSPHATE ION / Colicin-M immunity protein Function and homology information | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1.892 Å | ||||||
Authors | Zeth, K. / Patzer, S.I. / Albrecht, R. / Uson, I. / Braun, V. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2012 Title: The Crystal Structure of the Dimeric Colicin M Immunity Authors: Uson, I. / Patzer, S.I. / Dayana Rodriguez, D.D. / Braun, V. / Zeth, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4aeq.cif.gz | 51.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aeq.ent.gz | 37.1 KB | Display | PDB format |
PDBx/mmJSON format | 4aeq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4aeq_validation.pdf.gz | 437 KB | Display | wwPDB validaton report |
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Full document | 4aeq_full_validation.pdf.gz | 437.6 KB | Display | |
Data in XML | 4aeq_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 4aeq_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/4aeq ftp://data.pdbj.org/pub/pdb/validation_reports/ae/4aeq | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-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: 11670.021 Da / Num. of mol.: 1 / Fragment: RESIDUES 44-141 Source method: isolated from a genetically manipulated source Details: CMI CLONED WITHOUT THE N-TERMINAL HYDROPHOBIC HELIX FOR EXPRESSION OF THE PROTEIN IN THE CYTOPLASM Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P18002 |
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#2: Chemical | ChemComp-PO4 / |
#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: 2.26 Å3/Da / Density % sol: 45.65 % / Description: NONE |
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Crystal grow | Details: 0.2 M AMMONIUM SULFATE, 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→50 Å / Num. obs: 15884 / % possible obs: 96.6 % / Observed criterion σ(I): 2.5 / Redundancy: 2.6 % / Biso Wilson estimate: 23.36 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.89→2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.5 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: DIRECT METHODS Starting model: ALPHA HELIX Resolution: 1.892→28.224 Å / SU ML: 0.22 / σ(F): 2.03 / Phase error: 23.05 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.597 Å2 / ksol: 0.455 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.892→28.224 Å
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Refine LS restraints |
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LS refinement shell |
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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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