+Open data
-Basic information
Entry | Database: PDB / ID: 3rt5 | ||||||
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Title | Lysozyme in 30% propanol | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Globular protein / cytoplasmic vesicles(lysosomes) | ||||||
Function / homology | Function and homology information Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Sharma, P. / Solanki, A.K. / Ashish | ||||||
Citation | Journal: to be published Title: Crystal Structure of Lysozyme in 30% propanol Authors: Sharma, P. / Solanki, A.K. / Ashish | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rt5.cif.gz | 38.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rt5.ent.gz | 29.2 KB | Display | PDB format |
PDBx/mmJSON format | 3rt5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rt5_validation.pdf.gz | 458.7 KB | Display | wwPDB validaton report |
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Full document | 3rt5_full_validation.pdf.gz | 460.8 KB | Display | |
Data in XML | 3rt5_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 3rt5_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/3rt5 ftp://data.pdbj.org/pub/pdb/validation_reports/rt/3rt5 | HTTPS FTP |
-Related structure data
Related structure data | |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules X
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme |
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-Non-polymers , 6 types, 117 molecules
#2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-IPA / #4: Chemical | ChemComp-POL / | #5: Chemical | ChemComp-ACT / | #6: Chemical | ChemComp-CL / #7: 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: 1.96 Å3/Da / Density % sol: 37.18 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 3.8 Details: 40mM Sodium Acetate, 150mM Sodium chloride, 30% 2-propanol, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 15, 2010 / Details: Mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 12009 / Num. obs: 12009 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 24.61 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 42.8 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.096 / Mean I/σ(I) obs: 16 / Num. unique all: 578 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→25.358 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8717 / SU ML: 0.17 / Isotropic thermal model: Isotropic / σ(F): 0 / σ(I): 2 / Phase error: 18.82 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.04 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.517 e/Å3 | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.86 Å2 / Biso mean: 24.61 Å2 / Biso min: 15.38 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→25.358 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 99 %
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