+Open data
-Basic information
Entry | Database: PDB / ID: 6q8r | ||||||
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Title | HEW Lysozyme under 2 kbar of argon | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / lysozyme / argon / high pressure | ||||||
Function / homology | Function and homology information Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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 / FOURIER SYNTHESIS / Resolution: 1.7 Å | ||||||
Authors | Prange, T. / Carpentier, P. / Colloc'h, N. | ||||||
Citation | Journal: To be published Title: Labelling protein crystals by argon at 2 kbar Authors: Prange, T. / Carpentier, P. #1: Journal: Journal of Applied Crystallography / Year: 2016 Title: Gas-sensitive biological crystals processed in pressurized oxygen and krypton atmospheres: deciphering gas channels in proteins using a novel soak-and-freeze methodology Authors: Lafumat, B. / Mueller-Dieckmann, C. / Leonard, G. / Colloc'h, N. / Prange, T. / Giraud, T. / Dobias, F. / Royant, A. / van der Linden, P. / Carpentier, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q8r.cif.gz | 47.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q8r.ent.gz | 31.8 KB | Display | PDB format |
PDBx/mmJSON format | 6q8r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/6q8r ftp://data.pdbj.org/pub/pdb/validation_reports/q8/6q8r | HTTPS FTP |
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-Related structure data
Related structure data | 6q8sC 6qarC 6ra8C 5fstS 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#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 , 5 types, 223 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-AR / #5: Chemical | ChemComp-ACT / | #6: 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: 2.09 Å3/Da / Density % sol: 41 % / Description: DIAMOND SHAPE |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 10 % (W/V) NACL, 0.1 M ACETATE BUFFER PH 4.8. + 25 % (V/V) ETH-GLYCOL |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.7712 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2018 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7712 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40 Å / Num. obs: 12830 / % possible obs: 94.4 % / Redundancy: 18 % / CC1/2: 0.999 / Rrim(I) all: 0.083 / Net I/σ(I): 19.03 |
Reflection shell | Resolution: 1.7→1.78 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 930 / CC1/2: 0.887 / Rrim(I) all: 0.472 / % possible all: 58.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5FST Resolution: 1.7→38.95 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.73 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.107 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.007 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→38.95 Å
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Refine LS restraints |
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