+Open data
-Basic information
Entry | Database: PDB / ID: 1ayi | ||||||
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Title | COLICIN E7 IMMUNITY PROTEIN IM7 | ||||||
Components | COLICIN E IMMUNITY PROTEIN 7 | ||||||
Keywords | BACTERIOCIN / E COLICINS / PROTEIN-PROTEIN INTERACTIONS / DNASE INHIBITOR | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Dennis, C.A. / Pauptit, R.A. / Wallis, R. / James, R. / Moore, G.R. / Kleanthous, C. | ||||||
Citation | Journal: Biochem.J. / Year: 1998 Title: A structural comparison of the colicin immunity proteins Im7 and Im9 gives new insights into the molecular determinants of immunity-protein specificity. Authors: Dennis, C.A. / Videler, H. / Pauptit, R.A. / Wallis, R. / James, R. / Moore, G.R. / Kleanthous, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ayi.cif.gz | 28.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ayi.ent.gz | 18.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ayi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ayi_validation.pdf.gz | 359 KB | Display | wwPDB validaton report |
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Full document | 1ayi_full_validation.pdf.gz | 359 KB | Display | |
Data in XML | 1ayi_validation.xml.gz | 2.9 KB | Display | |
Data in CIF | 1ayi_validation.cif.gz | 4.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/1ayi ftp://data.pdbj.org/pub/pdb/validation_reports/ay/1ayi | HTTPS FTP |
-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
#1: Protein | Mass: 9906.963 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q03708 |
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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: 2.14 Å3/Da / Density % sol: 41 % | |||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.2 Details: USING THE HANGING DROP METHOD, PROTEIN (10MG/ML) WAS CRYSTALLISED BY MIXING AN EQUAL VOLUME OF PROTEIN WITH A SOLUTION CONTAINING 55% SATURATED DI-AMMONIUM PHOSPHATE AND 200MM TRIS PH7.2. ...Details: USING THE HANGING DROP METHOD, PROTEIN (10MG/ML) WAS CRYSTALLISED BY MIXING AN EQUAL VOLUME OF PROTEIN WITH A SOLUTION CONTAINING 55% SATURATED DI-AMMONIUM PHOSPHATE AND 200MM TRIS PH7.2. THE DROP WAS EQUILIBRATED AGAINST A WELL CONTAINING 100% SATURATED DI-AMMONIUM PHOSPHATE AT ROOM TEMPERATURE., vapor diffusion - hanging drop | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 25, 1995 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→15 Å / Num. obs: 5828 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 16.7 Å2 / Rsym value: 0.049 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2→2.18 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.156 / % possible all: 87 |
Reflection | *PLUS Num. measured all: 19772 / Rmerge(I) obs: 0.049 |
Reflection shell | *PLUS % possible obs: 87 % / Rmerge(I) obs: 0.156 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 10 ALIGNED NMR STRUCTURES OF COLICIN E9 IMMUNITY PROTEIN IM9 Resolution: 2→10 Å / Cross valid method: THROUGHOUT Details: X-PLOR WAS USED INITIALLY TO REFINE THE VERY INCOMPLETE STARTING MODEL FROM MOLECULAR REPLACEMENT. THE REFINEMENT USING SIMULATED ANNEALING AND POSITIONAL REFINEMENT DID NOT DECREASE THE ...Details: X-PLOR WAS USED INITIALLY TO REFINE THE VERY INCOMPLETE STARTING MODEL FROM MOLECULAR REPLACEMENT. THE REFINEMENT USING SIMULATED ANNEALING AND POSITIONAL REFINEMENT DID NOT DECREASE THE FREE R VALUE. AT THIS STAGE, REFINEMENT BY MAXIMUM LIKELIHOOD METHOD WAS STARTED.
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Displacement parameters | Biso mean: 21.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.178 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |