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Yorodumi- PDB-1c10: CRYSTAL STRUCTURE OF HEW LYSOZYME UNDER PRESSURE OF XENON (8 BAR) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c10 | ||||||
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Title | CRYSTAL STRUCTURE OF HEW LYSOZYME UNDER PRESSURE OF XENON (8 BAR) | ||||||
Components | PROTEIN (LYSOZYME) | ||||||
Keywords | HYDROLASE / HYDROPHOBIC CAVITY / XENON 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 / OTHER / 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: Biochem.Biophys.Res.Commun. / 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 | 1c10.cif.gz | 41 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c10.ent.gz | 26.9 KB | Display | PDB format |
PDBx/mmJSON format | 1c10.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/1c10 ftp://data.pdbj.org/pub/pdb/validation_reports/c1/1c10 | HTTPS FTP |
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-Related structure data
Related structure data | 1c1mC 1c3lC 1qtkC 1lseS 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
#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 | #5: Water | ChemComp-HOH / | Nonpolymer details | OCCUPANCY FACTORS WERE REFINED. THE FIRST SITE IS ON A SPECIAL POSSITION AND HENCE REAL OCCUPANCY ...OCCUPANCY FACTORS WERE REFINED. THE FIRST SITE IS ON A SPECIAL POSSITION AND HENCE REAL OCCUPANCY IS TWICE THE REFINED VALUE | |
-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 | pH: 5.5 / Details: SODIUM CHLORIDE, PH = 5.5 | ||||||||||||||||||||
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: 0.961 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 8, 1996 / Details: MULTILAYER MIRROR |
Radiation | Monochromator: SI (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.961 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→9.9 Å / Num. obs: 6454 / % possible obs: 79 % / Observed criterion σ(I): 4 / Redundancy: 5.1 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.03→2.15 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 4.3 / % possible all: 59 |
Reflection shell | *PLUS % possible obs: 59 % |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 1LSE Resolution: 2.03→9.9 Å / Num. parameters: 4285 / Num. restraintsaints: 4086 / σ(F): 4 / Stereochemistry target values: ENGH & HUBER / Details: USED WEIGHTED FULL MATRIX LEAST SQUARES PROCEDURE
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Refine analyze | Num. disordered residues: 0 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.03→9.9 Å
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Refine LS restraints |
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