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Yorodumi- PDB-1jtm: Alternative Structures of a Sequence Extended T4 Lysozyme Show th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jtm | ||||||
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Title | Alternative Structures of a Sequence Extended T4 Lysozyme Show that the Highly Conserved Beta-Sheet has Weak Intrinsic Folding Propensity | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE / SEQUENCE DUPLICATION / CONTEXT DEPENDENT FOLDING / SEQUENCE REPEAT | ||||||
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 / Resolution: 1.9 Å | ||||||
Authors | Sagermann, M. / Matthews, B.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Crystal Structures of a T4-lysozyme Duplication-extension Mutant Demonstrate that the Highly Conserved beta-Sheet Region has Low Intrinsic Folding Propensity Authors: Sagermann, M. / Matthews, B.W. #1: 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. #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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jtm.cif.gz | 46.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jtm.ent.gz | 32.3 KB | Display | PDB format |
PDBx/mmJSON format | 1jtm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jtm_validation.pdf.gz | 428.3 KB | Display | wwPDB validaton report |
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Full document | 1jtm_full_validation.pdf.gz | 433.5 KB | Display | |
Data in XML | 1jtm_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 1jtm_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/1jtm ftp://data.pdbj.org/pub/pdb/validation_reports/jt/1jtm | HTTPS FTP |
-Related structure data
Related structure data | 1jtnC 2lzmS C: citing same article (ref.) S: Starting model for refinement |
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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: 20221.203 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: E / Plasmid: PHS1403 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme |
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#2: Chemical | ChemComp-BME / |
-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 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 50MM TRIS-GLYCINE, 20% PEG 8000, 10% Isopropanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Details: used microseeding | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 170 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 21, 1999 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→17 Å / Num. all: 19736 / Num. obs: 19736 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 24.7 Å2 / Rsym value: 0.069 / Net I/σ(I): 3.9 |
Reflection shell | Resolution: 1.9→2.01 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 2714 / Rsym value: 0.26 / % possible all: 99.8 |
Reflection | *PLUS Rmerge(I) obs: 0.068 |
-Processing
Software |
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Refinement | Starting model: PDB ID 2LZM Resolution: 1.9→17 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The structure was refined in the absence of water molecules. Only a BME molecule and a polyalanine peptide chain was fitted into difference density. The inserted polyalanine refined to a ...Details: The structure was refined in the absence of water molecules. Only a BME molecule and a polyalanine peptide chain was fitted into difference density. The inserted polyalanine refined to a grouped occupancy of ca. 0.3. Other less clear difference densities were observed as well but not fitted. The fitted chain was labeled with chain B. The connection of this chain to the c-terminus of the molecule is in very weak density and was not modeled.The former c-terminal residues Asn163 and Leu164 could were not detectable as well. Combination of CNS, BUSTER and TNT used for refinement.
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→17 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.9 Å / Rfactor all: 0.219 / Rfactor obs: 0.214 / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.214 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_angle_deg / Dev ideal: 1.4 |