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Yorodumi- PDB-3jr6: Sequential reorganization of beta-sheet topology by insertion of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jr6 | |||||||||
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Title | Sequential reorganization of beta-sheet topology by insertion of a single strand | |||||||||
Components | Lysozyme | |||||||||
Keywords | HYDROLASE / sequence duplication / protein design / tandem repeat / beta-sheet / Antimicrobial / Bacteriolytic enzyme / Glycosidase | |||||||||
Function / homology | Function and homology information viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium Similarity search - Function | |||||||||
Biological species | Enterobacteria phage T4 (virus) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Sagermann, M. / Baas, W.A. / Matthews, B.W. | |||||||||
Citation | Journal: Protein Sci. / Year: 2006 Title: Sequential reorganization of beta-sheet topology by insertion of a single strand. Authors: Sagermann, M. / Baase, W.A. / Matthews, B.W. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: Long-distance conformational changes in a protein engineered by modulated sequence duplication. Authors: Sagermann, M. / Gay, L. / Matthews, B.W. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999 Title: Structural characterization of an engineered tandem repeat contrasts the importance of context and sequence in protein folding. Authors: Sagermann, M. / Baase, W.A. / Matthews, B.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jr6.cif.gz | 128.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jr6.ent.gz | 101.9 KB | Display | PDB format |
PDBx/mmJSON format | 3jr6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jr6_validation.pdf.gz | 467.5 KB | Display | wwPDB validaton report |
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Full document | 3jr6_full_validation.pdf.gz | 514.9 KB | Display | |
Data in XML | 3jr6_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 3jr6_validation.cif.gz | 40.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/3jr6 ftp://data.pdbj.org/pub/pdb/validation_reports/jr/3jr6 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 19220.088 Da / Num. of mol.: 4 Mutation: C54T, C97A, insertion of seuqence (gighll) after residue L33 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: E / Plasmid: phs 1403 / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme #2: Chemical | ChemComp-SO4 / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.29 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 3400, 50 mM ammonium sulfate, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 5, 1998 / Details: yale mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3→32.44 Å / Num. obs: 17925 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rsym value: 0.07 |
Reflection shell | Highest resolution: 3 Å / Rsym value: 0.097 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: T4 lysozyme I3P mutant Resolution: 3→32.44 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Authors state that scaling and B-value refinement were performed with CNS using a recommended resolution range of 6.0-3.0 A resolution. As the B-values for the data set were determined to be ...Details: Authors state that scaling and B-value refinement were performed with CNS using a recommended resolution range of 6.0-3.0 A resolution. As the B-values for the data set were determined to be low (even for higher low-resolution cut-offs), the B-values for the atoms remained similarly low as well. Molecules A and B exhibit well-defined density of the loops. The corresponding loops of molecules B and C were in poor density but could clearly be identified. Loops and terminal residues that could not be refined reliably were omitted: B(L170), D(L170), B(34-46), C(36-46).
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3→32.44 Å
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Refine LS restraints |
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