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Yorodumi- PDB-1sx7: Use of an ion-binding site to bypass the 1000-atom limit to ab in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sx7 | ||||||
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Title | Use of an ion-binding site to bypass the 1000-atom limit to ab initio structure determination by direct methods | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / ab initio direct methods | ||||||
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: 1.06 Å | ||||||
Authors | Mooers, B.H.M. / Matthews, B.W. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Use of an ion-binding site to bypass the 1000-atom limit to structure determination by direct methods. Authors: Mooers, B.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 | 1sx7.cif.gz | 101.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sx7.ent.gz | 76 KB | Display | PDB format |
PDBx/mmJSON format | 1sx7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/1sx7 ftp://data.pdbj.org/pub/pdb/validation_reports/sx/1sx7 | HTTPS FTP |
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-Related structure data
Related structure data | 1swyC 1swzC 1sx2C 1lw9S 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: 18590.377 Da / Num. of mol.: 1 / Mutation: D72A, R96E 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: PH1403 / Cell line (production host): RR101 / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme | ||||||
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#2: Chemical | ChemComp-RB / #3: Chemical | ChemComp-CL / #4: Chemical | #5: 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: 2.6 Å3/Da / Density % sol: 52.41 % |
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Crystal grow | pH: 6.7 Details: sodium:potassium phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 100K, pH 6.70 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.773 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 4, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.773 Å / Relative weight: 1 |
Reflection | Resolution: 1.06→22 Å / Num. obs: 87349 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.06→1.12 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 4 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LW9 Resolution: 1.06→22 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: ATOMS OUT OF DENSITY REMOVED. RESIDUES 55 AND 162-164 ARE VERY DISORDERED.
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Solvent computation | Solvent model: SWAT 1 0.88759 SWAT 2 3.31777 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.06→22 Å
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Refine LS restraints |
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