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Yorodumi- PDB-1qtk: CRYSTAL STRUCTURE OF HEW LYSOZYME UNDER PRESSURE OF KRYPTON (55 BAR) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qtk | ||||||
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Title | CRYSTAL STRUCTURE OF HEW LYSOZYME UNDER PRESSURE OF KRYPTON (55 BAR) | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE / HYDROPHOBIC CAVITY / KRYPTON COMPLEX | ||||||
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 / Resolution: 2.03 Å | ||||||
Authors | Prange, T. / Schiltz, M. / Pernot, L. / Colloc'h, N. / Longhi, S. / Bourguet, W. / Fourme, R. | ||||||
Citation | Journal: Proteins / Year: 1998 Title: Exploring hydrophobic sites in proteins with xenon or krypton. Authors: Prange, T. / Schiltz, M. / Pernot, L. / Colloc'h, N. / Longhi, S. / Bourguet, W. / Fourme, R. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1995 Title: The Influence of Temperature on Lysozyme Crystals. Structure and Dynamics of Protein and Water. Authors: Kurinov, I.V. / Harrison, R.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qtk.cif.gz | 35.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qtk.ent.gz | 26.7 KB | Display | PDB format |
PDBx/mmJSON format | 1qtk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/1qtk ftp://data.pdbj.org/pub/pdb/validation_reports/qt/1qtk | HTTPS FTP |
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-Related 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
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Cell: EGG / Cellular location: EGG WHITE / References: UniProt: P00698, lysozyme | ||||
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#2: Chemical | ChemComp-NA / | ||||
#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-KR / | #5: 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: 2.03 Å3/Da / Density % sol: 39.4 % | ||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Sodium chloride , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 5 / Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.962 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 10, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.962 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→9.9 Å / Num. all: 8010 / Num. obs: 7734 / % possible obs: 80 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.8 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.03→2.15 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.141 / Num. unique all: 554 / % possible all: 63 |
Reflection shell | *PLUS % possible obs: 63 % |
-Processing
Software |
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Refinement | Resolution: 2.03→9.9 Å / σ(F): 3 / σ(I): 3 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure
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Refinement step | Cycle: LAST / Resolution: 2.03→9.9 Å
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Refine LS restraints |
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