+Open data
-Basic information
Entry | Database: PDB / ID: 2a4t | ||||||
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Title | Crystal structure of spin labeled T4 Lysozyme (V131R7) | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / NITROXIDE SPIN LABEL / EPR / MODIFIED CYSTEINE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Fleissner, M.R. / Cascio, D. / Sawaya, M.R. / Hideg, K. / Hubbell, W.L. | ||||||
Citation | Journal: To be Published Title: Crystal structure of spin labeled T4 Lysozyme (V131R7 Authors: Fleissner, M.R. / Cascio, D. / Sawaya, M.R. / Hideg, K. / Hubbell, W.L. #1: Journal: Biochemistry / Year: 2000 Title: Crystal structures of spin labeled T4 lysozyme mutants: implications for the interpretation of EPR spectra in terms of structure. Authors: Langen, R. / Oh, K.J. / Cascio, D. / Hubbell, W.L. | ||||||
History |
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Remark 600 | HETEROGEN THE POSITIONS OF THE ATOMS OF THE NITROXIDE RING OF R7A ARE NOT UNIQUE, AS THOSE ...HETEROGEN THE POSITIONS OF THE ATOMS OF THE NITROXIDE RING OF R7A ARE NOT UNIQUE, AS THOSE PARTICULAR ATOMS WERE NOT RESOLVED IN EITHER CONFORMATION (A OR B). COORDINATES FOR ATOMS OF THE NITROXIDE RING WERE DEPOSITED IN A MINIMUM ENERGY CONFIGURATION. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a4t.cif.gz | 55.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a4t.ent.gz | 37.6 KB | Display | PDB format |
PDBx/mmJSON format | 2a4t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/2a4t ftp://data.pdbj.org/pub/pdb/validation_reports/a4/2a4t | HTTPS FTP |
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-Related structure data
Related structure data | 1c6tS 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: 18632.375 Da / Num. of mol.: 1 / Mutation: C54T,C97A,V131C 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 (bacteria) / Strain (production host): BL21 / References: UniProt: P00720, lysozyme |
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-Non-polymers , 5 types, 254 molecules
#2: Chemical | ChemComp-R7A / | ||||
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#3: Chemical | ChemComp-AZI / | ||||
#4: Chemical | #5: Chemical | ChemComp-HED / | #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: 2.65 Å3/Da / Density % sol: 53.56 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: potassium phosphate, sodium phospahte, sodium choloride, sodium azide, oxidized beta-mercaptoehtanol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 273K |
-Data collection
Diffraction | Mean temperature: 100 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: Feb 28, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→80 Å / Num. all: 22428 / Num. obs: 22403 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 28.7 Å2 / Rsym value: 0.059 / Χ2: 1.106 / Net I/σ(I): 32.9 |
Reflection shell | Resolution: 1.7→1.76 Å / % possible obs: 99.7 % / Redundancy: 6.3 % / Mean I/σ(I) obs: 5.3 / Num. measured obs: 2221 / Num. unique all: 2221 / Rsym value: 0.303 / Χ2: 0.805 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1C6T Resolution: 1.7→51.78 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 1.696 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.103 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.987 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→51.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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