+Open data
-Basic information
Entry | Database: PDB / ID: 3g3w | ||||||
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Title | Crystal structure of spin labeled T4 Lysozyme (T151R1) at 291 K | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / MODIFIED CYSTEINE / NITROXIDE / Antimicrobial / Bacteriolytic enzyme / Glycosidase | ||||||
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 / Resolution: 2.3 Å | ||||||
Authors | Fleissner, M.R. / Cascio, D. / Hubbell, W.L. | ||||||
Citation | Journal: Protein Sci. / Year: 2009 Title: Structural origin of weakly ordered nitroxide motion in spin-labeled proteins. Authors: Fleissner, M.R. / Cascio, D. / Hubbell, W.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g3w.cif.gz | 48.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g3w.ent.gz | 32.9 KB | Display | PDB format |
PDBx/mmJSON format | 3g3w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g3w_validation.pdf.gz | 890.7 KB | Display | wwPDB validaton report |
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Full document | 3g3w_full_validation.pdf.gz | 890.8 KB | Display | |
Data in XML | 3g3w_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 3g3w_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/3g3w ftp://data.pdbj.org/pub/pdb/validation_reports/g3/3g3w | HTTPS FTP |
-Related structure data
Related structure data | 1zytC 2cuuC 3g3vC 3g3xC 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18630.402 Da / Num. of mol.: 1 / Mutation: C54T, C97A, T151C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: E, Lysozyme / Plasmid: pHSe5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P00720, lysozyme |
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-Non-polymers , 5 types, 45 molecules
#2: Chemical | ChemComp-MTN / |
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#3: Chemical | ChemComp-HED / |
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-AZI / |
#6: 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: 2.75 Å3/Da / Density % sol: 55.26 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 2.0M dibasic potassium phosphate and monobasic sodium phospahte, 0.25M sodium choloride, 0.04% sodium azide, 0.02M oxidized beta-mercaptoehtanol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 22, 2007 / Details: Confocal 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: 2.3→80 Å / Num. all: 28187 / Num. obs: 9516 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rsym value: 0.159 / Χ2: 1.901 / Net I/σ(I): 9.626 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 925 / Rsym value: 0.501 / Χ2: 2.012 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Starting model: PDB ENTRY 1C6T Resolution: 2.3→26.265 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.85 / σ(F): 0 / Stereochemistry target values: ml
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Solvent computation | Bsol: 44.842 Å2 / ksol: 0.355 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 147.12 Å2 / Biso mean: 26.405 Å2 / Biso min: 3.35 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→26.265 Å
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Refine LS restraints |
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LS refinement shell |
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