+Open data
-Basic information
Entry | Database: PDB / ID: 2hul | ||||||
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Title | Crystal structure of T4 Lysozyme S44C synthetic dimer | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / T4 Lysozyme synthetic dimer | ||||||
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: 1.8 Å | ||||||
Authors | Banatao, D.R. / Cascio, D. / Yeates, T.O. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: An approach to crystallizing proteins by synthetic symmetrization. Authors: Banatao, D.R. / Cascio, D. / Crowley, C.S. / Fleissner, M.R. / Tienson, H.L. / Yeates, T.O. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE. THE BIOLOGICAL UNIT IS A DIMER FORMED BY DISULFIDE BOND BETWEEN CYSTEINES 44. THE DISULFIDE BOND OVERLAPS WITH THE CRYSTALLOGRAPHIC 2-FOLD AXIS. THE DIMER IS A SYMMETRICAL DIMER. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hul.cif.gz | 52.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hul.ent.gz | 36 KB | Display | PDB format |
PDBx/mmJSON format | 2hul.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hul_validation.pdf.gz | 438.7 KB | Display | wwPDB validaton report |
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Full document | 2hul_full_validation.pdf.gz | 440.1 KB | Display | |
Data in XML | 2hul_validation.xml.gz | 10 KB | Display | |
Data in CIF | 2hul_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/2hul ftp://data.pdbj.org/pub/pdb/validation_reports/hu/2hul | HTTPS FTP |
-Related structure data
Related structure data | 2hukC 2humC 1c6tS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18644.428 Da / Num. of mol.: 1 / Mutation: S44C 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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00720, lysozyme | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: 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: 2.78 Å3/Da / Density % sol: 55.72 % Description: Terminal residues 163 and 164 for T4 lysozyme have poor electron density. This should be taken into account when using this structure as a model. |
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Crystal grow | Temperature: 298 K / pH: 6.7 Details: 2.0 M Ammonium Sulfate, 0.1 M Cacodylate pH 6.7, 0.2 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.70 |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: May 26, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→77.38 Å / Num. obs: 19413 / % possible obs: 99.1 % / Rsym value: 0.056 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.5→1.55 Å / Mean I/σ(I) obs: 4.2 / Rsym value: 0.302 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1C6T Resolution: 1.8→40.32 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.048 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.114 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DIFFERENCE MAPS SHOW THAT DISULFIDE BONDS ARE PARTIALLY BROKEN DUE TO SYNCHOTRON RADIATION. THE PRESENCE OF DISULFIDE BONDS WAS CONFIRMED ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DIFFERENCE MAPS SHOW THAT DISULFIDE BONDS ARE PARTIALLY BROKEN DUE TO SYNCHOTRON RADIATION. THE PRESENCE OF DISULFIDE BONDS WAS CONFIRMED BY GEL ELECTROPHORESIS AND CHROMATOGRAPHY PRIOR TO CRYSTALLIZATION. FOR MORE INFORMATION ON THIS PHENOMENON WE REFER TO: BANUMATHI ET AL. "STRUCTURAL EFFECTS OF RADIATION DAMAGE AND ITS POTENTIAL FOR PHASING", ACTA CRYST.(D60),1085-93,2004.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.78 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→40.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.85 Å / Total num. of bins used: 20
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