|Entry||Database: PDB / ID: 1jtm|
|Title||Alternative Structures of a Sequence Extended T4 Lysozyme Show that the Highly Conserved Beta-Sheet has Weak Intrinsic Folding Propensity|
|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 / killing of cells of another organism / defense response to bacterium / host cell cytoplasm
Similarity search - Function
Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Endolysin
Similarity search - Component
|Biological species||Enterobacteria phage T4 (virus)|
|Method||X-RAY DIFFRACTION / Resolution: 1.9 Å|
|Authors||Sagermann, M. / Matthews, B.W.|
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.
|Structure viewer||Molecule: |
-Downloads & links
|PDBx/mmCIF format||1jtm.cif.gz||41.8 KB||Display||PDBx/mmCIF format|
|PDB format||pdb1jtm.ent.gz||32.3 KB||Display||PDB format|
|PDBx/mmJSON format||1jtm.json.gz||Tree view||PDBx/mmJSON format|
|Summary document||1jtm_validation.pdf.gz||427.5 KB||Display||wwPDB validaton report|
|Full document||1jtm_full_validation.pdf.gz||432.6 KB||Display|
|Data in XML||1jtm_validation.xml.gz||9.1 KB||Display|
|Data in CIF||1jtm_validation.cif.gz||11.3 KB||Display|
-Related structure data
|Related structure data|
C: citing same article (ref.)
S: Starting model for refinement
|Similar structure data|
|PDB pages||PDBj / wwPDB / NCBI|
|Related items in Molecule of the Month|
|#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
|#2: Chemical|| ChemComp-BME / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 2.75 Å3/Da / Density % sol: 55 %|
|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
*PLUSpH: 7.5 / Details: used microseeding
|Components of the solutions|
|Diffraction||Mean temperature: 170 K|
|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|
*PLUSRmerge(I) obs: 0.068
|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.
|Refinement step||Cycle: LAST / Resolution: 1.9→17 Å|
|Refine LS restraints|
*PLUSHighest resolution: 1.9 Å / Rfactor all: 0.219 / Rfactor obs: 0.214 / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.214
|Refine LS restraints|
*PLUSType: t_angle_deg / Dev ideal: 1.4
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