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Yorodumi- PDB-2zrr: Crystal structure of an immunity protein that contributes to the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zrr | ||||||
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Title | Crystal structure of an immunity protein that contributes to the self-protection of bacteriocin-producing Enterococcus mundtii 15-1A | ||||||
Components | Mundticin KS immunity protein | ||||||
Keywords | ANTIMICROBIAL PROTEIN / antiparallel four-helix bundle | ||||||
Function / homology | de novo design (two linked rop proteins) - #140 / Lactococcin-A immunity protein-like / Enterocin A Immunity / de novo design (two linked rop proteins) / Up-down Bundle / Mainly Alpha / Mundticin KS immunity protein Function and homology information | ||||||
Biological species | Enterococcus mundtii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å | ||||||
Authors | Jeon, H.J. / Noda, M. / Matoba, Y. / Kumagai, T. / Sugiyama, M. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2009 Title: Crystal structure and mutagenic analysis of a bacteriocin immunity protein, Mun-im Authors: Jeon, H.J. / Noda, M. / Matoba, Y. / Kumagai, T. / Sugiyama, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zrr.cif.gz | 30.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zrr.ent.gz | 19.9 KB | Display | PDB format |
PDBx/mmJSON format | 2zrr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/2zrr ftp://data.pdbj.org/pub/pdb/validation_reports/zr/2zrr | 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: 13290.209 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus mundtii (bacteria) / Strain: 15-1A / Gene: orf8 / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: B9A7V6*PLUS |
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#2: Water | ChemComp-HOH / |
Sequence details | THE SEQUNECE DATABSE OF THIS PROTEIN HAS BEEN DEPOSITED TO DDBJ. ACCESSION CODE AB454504. IT WILL ...THE SEQUNECE DATABSE OF THIS PROTEIN HAS BEEN DEPOSITED TO DDBJ. ACCESSION CODE AB454504. IT WILL BE OPENED WHEN THIS FILE IS PUBLISHED. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.85 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 3.5 Details: 3.1M sodium formate, 0.1M sodium citrate, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 9, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→100 Å / Num. all: 9138 / Num. obs: 9138 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 39.7 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 1.8 / Num. unique all: 644 / Rsym value: 0.368 / % possible all: 69.4 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.8→10 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 49.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.88 Å / Rfactor Rfree error: 0.076 / Total num. of bins used: 10
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Xplor file |
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