+Open data
-Basic information
Entry | Database: PDB / ID: 7avf | ||||||
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Title | Triclinic hydrogenated hen egg-white lysozyme at 100 K (control) | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / lysozyme / hewl / hydrogenated | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å | ||||||
Authors | Ramos, J. / Laux, V. / Haertlein, M. / Erba Boeri, E. / Forsyth, V.T. / Mossou, E. / Larsen, S. / Langkilde, A.E. | ||||||
Citation | Journal: Iucrj / Year: 2021 Title: Structural insights into protein folding, stability and activity using in vivo perdeuteration of hen egg-white lysozyme. Authors: Ramos, J. / Laux, V. / Haertlein, M. / Boeri Erba, E. / McAuley, K.E. / Forsyth, V.T. / Mossou, E. / Larsen, S. / Langkilde, A.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7avf.cif.gz | 131.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7avf.ent.gz | 87.3 KB | Display | PDB format |
PDBx/mmJSON format | 7avf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7avf_validation.pdf.gz | 454 KB | Display | wwPDB validaton report |
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Full document | 7avf_full_validation.pdf.gz | 454.1 KB | Display | |
Data in XML | 7avf_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 7avf_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/7avf ftp://data.pdbj.org/pub/pdb/validation_reports/av/7avf | HTTPS FTP |
-Related structure data
Related structure data | 7aveC 7avgC 4yeoS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Production host: Gallus gallus (chicken) / References: UniProt: P00698, lysozyme | ||||||
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#2: Chemical | ChemComp-NO3 / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.7 Å3/Da / Density % sol: 27.84 % |
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Crystal grow | Temperature: 291 K / Method: batch mode / pH: 4.5 / Details: sodium nitrate, sodium acetate pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.7293 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7293 Å / Relative weight: 1 |
Reflection | Resolution: 1→31.99 Å / Num. obs: 50297 / % possible obs: 97.47 % / Redundancy: 3.5 % / Biso Wilson estimate: 8.43 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.0727 / Rpim(I) all: 0.0449 / Rrim(I) all: 0.0856 / Net I/σ(I): 9.25 |
Reflection shell | Resolution: 1→1.036 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2.81 / Num. unique obs: 4908 / CC1/2: 0.884 / Rpim(I) all: 0.236 / Rrim(I) all: 0.453 / % possible all: 94.95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4yeo Resolution: 1→31.99 Å / SU ML: 0.0791 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 12.9428 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→31.99 Å
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Refine LS restraints |
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LS refinement shell |
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