[English] 日本語
Yorodumi- PDB-1vdq: The crystal structure of the orthorhombic form of hen egg white l... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vdq | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of the orthorhombic form of hen egg white lysozyme at 1.5 angstroms resolution | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / lysozyme / hen egg white / orthrhombic | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Aibara, S. / Suzuki, A. / Kidera, A. / Shibata, K. / Yamane, T. / DeLucas, L.J. / Hirose, M. | ||||||
Citation | Journal: to be published Title: The crystal structure of the orthorhombic form of hen egg white lysozyme at 1.5 angstroms resolution Authors: Aibara, S. / Suzuki, A. / Kidera, A. / Shibata, K. / Yamane, T. / DeLucas, L.J. / Hirose, M. #1: Journal: Proceedings of the Twenty-Third International Symposium on Space Technology and Science Year: 2002 Title: Microgravity Influences the Nucleation Process of Protein Crystal Growth Authors: Aibara, S. / Suzuki, A. / Kidera, A. / Shibata, K. / Yamane, T. / DeLucas, L.J. / Hirose, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1vdq.cif.gz | 38.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1vdq.ent.gz | 26.5 KB | Display | PDB format |
PDBx/mmJSON format | 1vdq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/1vdq ftp://data.pdbj.org/pub/pdb/validation_reports/vd/1vdq | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: Egg White / References: UniProt: P00698, lysozyme |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.12 % |
---|---|
Crystal grow | Method: batch method / Details: batch method |
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: May 12, 1998 |
Radiation | Monochromator: Confocal Mirror MicroMax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→22.8 Å / Num. all: 18736 / Num. obs: 18736 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.054 |
Reflection shell | Resolution: 1.5→1.55 Å / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 9.2 / % possible all: 87.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→22.83 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 14150001.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: protein_rep.param
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.354 Å2 / ksol: 0.374607 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.4 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→22.83 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|