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Yorodumi- PDB-1jqu: Are Carboxy Terminii of Helices Coded by the Local Sequence or by... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jqu | ||||||
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Title | Are Carboxy Terminii of Helices Coded by the Local Sequence or by Tertiary Structure Contacts | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / glycine helix terminii / Schellman motif / alpha-L motif | ||||||
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: 2.6 Å | ||||||
Authors | Sagermann, M. / Martensson, L.-G. / Baase, W.A. / Matthews, B.W. | ||||||
Citation | Journal: Protein Sci. / Year: 2002 Title: A test of proposed rules for helix capping: Implications for protein design Authors: Sagermann, M. / Martensson, L.-G. / Baase, W.A. / Matthews, B.W. #1: Journal: Science / Year: 1994 Title: Rules for alpha-helix termination by glycine. Authors: Aurora, R. / Srinivasan, R. / Rose, G.D. #2: Journal: Protein Folding / Year: 1980 Title: The alpha-L Conformations at the Ends of Helices Authors: Schellman, C. #3: 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 | 1jqu.cif.gz | 140.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jqu.ent.gz | 110.8 KB | Display | PDB format |
PDBx/mmJSON format | 1jqu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jqu_validation.pdf.gz | 456.2 KB | Display | wwPDB validaton report |
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Full document | 1jqu_full_validation.pdf.gz | 537.9 KB | Display | |
Data in XML | 1jqu_validation.xml.gz | 35.3 KB | Display | |
Data in CIF | 1jqu_validation.cif.gz | 46.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/1jqu ftp://data.pdbj.org/pub/pdb/validation_reports/jq/1jqu | HTTPS FTP |
-Related structure data
Related structure data | 1llhC 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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2 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 18555.312 Da / Num. of mol.: 4 / Mutation: C54T, C97A, W158L 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: Water | ChemComp-HOH / | |
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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: 2.67 Å3/Da / Density % sol: 53.93 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.75 Details: 30% PEG4000, PIPES buffer ph7.0, 0.2M LiSO4, pH 6.75, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Nov 14, 1995 |
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: 2.6→34.9 Å / Num. all: 22095 / Num. obs: 22095 / % possible obs: 79 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.42 % / Biso Wilson estimate: 36 Å2 / Rsym value: 0.057 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 3983 / Rsym value: 0.257 / % possible all: 71.5 |
Reflection | *PLUS % possible obs: 78 % / Rmerge(I) obs: 0.057 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: T4 Lysozyme 2LZM Resolution: 2.6→35 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Molecular replacement (direct rotation searches) was carried out with lysozyme search molecules with different hinge bending-angles. The starting model was subjected to several rounds of CNS ...Details: Molecular replacement (direct rotation searches) was carried out with lysozyme search molecules with different hinge bending-angles. The starting model was subjected to several rounds of CNS SA-refinement and subsequently refined with TNT. Positve density was observed around crystal contact sites. These features, presumably PEG molecules, could not be modeled unambigously and were therefore omitted from the final model.
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.6→35 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.6 Å / σ(F): 0 / Rfactor all: 0.241 / Rfactor obs: 0.235 / Rfactor Rfree: 0.315 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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