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- PDB-1jqu: Are Carboxy Terminii of Helices Coded by the Local Sequence or by... -
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Open data
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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 | ||||||
![]() | Lysozyme | ||||||
![]() | HYDROLASE / glycine helix terminii / Schellman motif / alpha-L motif | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sagermann, M. / Martensson, L.-G. / Baase, W.A. / Matthews, B.W. | ||||||
![]() | ![]() 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: ![]() Title: The alpha-L Conformations at the Ends of Helices Authors: Schellman, C. #3: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.2 KB | Display | ![]() |
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PDB format | ![]() | 110.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.2 KB | Display | ![]() |
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Full document | ![]() | 537.9 KB | Display | |
Data in XML | ![]() | 35.3 KB | Display | |
Data in CIF | ![]() | 46.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1llhC ![]() 2lzmS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 18555.312 Da / Num. of mol.: 4 / Mutation: C54T, C97A, W158L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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