+Open data
-Basic information
Entry | Database: PDB / ID: 1p56 | ||||||
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Title | Duplication-extension of Helix A of T4 lysozyme | ||||||
Components | PROTEIN (Lysozyme) | ||||||
Keywords | HYDROLASE / sequence duplication / folding propensity / completion folding experiment | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Sagermann, M. / Gay, L. / Baase, W.A. / Matthews, B.W. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Relocation or duplication of the helix A sequence of T4 lysozyme causes only modest changes in structure but can increase or decrease the rate of folding. Authors: Sagermann, M. / Baase, W.A. / Mooers, B.H. / Gay, L. / Matthews, B.W. #1: Journal: J.Mol.Biol. / Year: 2002 Title: Crystal structures of a T4-lysozyme duplication-extension mutant demonstrates that the highly conserved beta-sheet region has low intrinsic folding propensity Authors: Sagermann, M. / Matthews, B.W. #2: Journal: J.Mol.Biol. / Year: 1987 Title: Structure of bacteriophage T4 lysozyme refined at 1.7 A resolution Authors: Weaver, L.H. / Matthews, B.W. #3: 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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Remark 999 | SEQUENCE Residue Leu 164 was deleted and sequence SGGAMNIFEMLRIDE was appended to the C-terminus |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p56.cif.gz | 48.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p56.ent.gz | 33.7 KB | Display | PDB format |
PDBx/mmJSON format | 1p56.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p56_validation.pdf.gz | 428.6 KB | Display | wwPDB validaton report |
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Full document | 1p56_full_validation.pdf.gz | 434 KB | Display | |
Data in XML | 1p56_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 1p56_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/1p56 ftp://data.pdbj.org/pub/pdb/validation_reports/p5/1p56 | HTTPS FTP |
-Related structure data
Related structure data | 1p5cC 2lzmS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 19953.857 Da / Num. of mol.: 1 / Mutation: C54T, C97A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: Gene product E / Plasmid: phs1403 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme |
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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: 2.75 Å3/Da / Density % sol: 55.25 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 35% PEG 4000, 50mM phosphate buffer, 5% isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 170 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.999 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 10, 2002 / Details: mirrors |
Radiation | Monochromator: Flat mirror, single SI crystal bend / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→28.75 Å / Num. obs: 22444 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 14.24 Å2 / Rsym value: 0.066 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.79→1.9 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 5.1 / Num. unique all: 3053 / Rsym value: 0.11 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2LZM Resolution: 1.8→30 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Only disconnected density could be seen in the vicinity of the old c-terminus. Therefore, the sequence of the appended residues SGGAMNIFEMLRIDE could not be placed reliably into the density ...Details: Only disconnected density could be seen in the vicinity of the old c-terminus. Therefore, the sequence of the appended residues SGGAMNIFEMLRIDE could not be placed reliably into the density and was omitted in the final model.
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Displacement parameters | Biso mean: 0.74 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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