+Open data
-Basic information
Entry | Database: PDB / ID: 2nw0 | ||||||
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Title | Crystal structure of a lysin | ||||||
Components | PlyB | ||||||
Keywords | HYDROLASE / Beta Barrel | ||||||
Function / homology | Glycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / ACETATE ION Function and homology information | ||||||
Biological species | unidentified phage (virus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Porter, C.J. / Buckle, A.M. / Whisstock, J.C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: The 1.6 A Crystal Structure of the Catalytic Domain of PlyB, a Bacteriophage Lysin Active Against Bacillus anthracis. Authors: Porter, C.J. / Schuch, R. / Pelzek, A.J. / Buckle, A.M. / McGowan, S. / Wilce, M.C. / Rossjohn, J. / Russell, R. / Nelson, D. / Fischetti, V.A. / Whisstock, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nw0.cif.gz | 99.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nw0.ent.gz | 75.7 KB | Display | PDB format |
PDBx/mmJSON format | 2nw0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/2nw0 ftp://data.pdbj.org/pub/pdb/validation_reports/nw/2nw0 | HTTPS FTP |
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-Related structure data
Related structure data | 1jfxS 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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Details | The biological unit is a monomer |
-Components
#1: Protein | Mass: 21516.100 Da / Num. of mol.: 2 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified phage (virus) / Strain: BcpI / Gene: PlyB / Plasmid: pBAD24 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: lysozyme #2: Chemical | ChemComp-ACT / #3: 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: 1.88 Å3/Da / Density % sol: 34.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.6 Details: 32% PEG 4000, 0.1M sodium acetate, 0.2M ammonium acetate, 0.009M Copper (2) chloride, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 11, 2006 / Details: osmic mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→66.52 Å / Num. obs: 47219 / % possible obs: 92.3 % / Redundancy: 6.2 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 4 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 1.5 / Num. measured all: 16065 / Num. unique all: 4014 / Rsym value: 0.498 / % possible all: 54.3 |
-Phasing
Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JFX Resolution: 1.6→66.519 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.237 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.937 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→66.519 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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Refinement TLS params. | S21: 0.0019 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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