[English] 日本語
Yorodumi- PDB-1xft: Synchrotron X-ray Powder Diffraction Study of Hexagonal Turkey Eg... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xft | ||||||
---|---|---|---|---|---|---|---|
Title | Synchrotron X-ray Powder Diffraction Study of Hexagonal Turkey Egg-white Lysozyme | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / powder diffraction / lysozyme / x-rays | ||||||
Function / homology | Function and homology information glycosaminoglycan binding / 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 / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Meleagris gallopavo (turkey) | ||||||
Method | POWDER DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å | ||||||
Authors | Margiolaki, I. / Wright, J.P. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Synchrotron X-ray powder diffraction study of hexagonal turkey egg-white lysozyme. Authors: Margiolaki, I. / Wright, J.P. / Fitch, A.N. / Fox, G.C. / Von Dreele, R.B. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Binding of N-acetylglucosamine to chicken egg lysozyme: a powder diffraction study Authors: Von Dreele, R.B. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1995 Title: Structure of hexagonal turkey egg-white lysozyme at 1.65A resolution Authors: Howell, P.L. #3: Journal: Acta Crystallogr.,Sect.D / Year: 1993 Title: X-ray structure of monoclinic turkey egg lysozyme at 1.3 A resolution Authors: Harata, K. #4: Journal: Acta Crystallogr.,Sect.B / Year: 1992 Title: Structure determination of turkey egg-white lysozyme using Laue diffraction data Authors: Howell, P.L. / Almo, S.C. / Parsons, M.R. / Hajdu, J. / Petsko, G.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1xft.cif.gz | 33.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1xft.ent.gz | 19.9 KB | Display | PDB format |
PDBx/mmJSON format | 1xft.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xft_validation.pdf.gz | 342.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1xft_full_validation.pdf.gz | 373 KB | Display | |
Data in XML | 1xft_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 1xft_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xf/1xft ftp://data.pdbj.org/pub/pdb/validation_reports/xf/1xft | HTTPS FTP |
-Related structure data
Related structure data | 1tewS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 14228.105 Da / Num. of mol.: 1 / Fragment: LYSOZYME / Source method: isolated from a natural source / Details: sigma-aldrich chemical company LOT. 064H7230 / Source: (natural) Meleagris gallopavo (turkey) / Tissue: egg white / References: UniProt: P00703, lysozyme |
---|
-Experimental details
-Experiment
Experiment | Method: POWDER DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 44.81 % |
---|---|
Crystal grow | Temperature: 295 K / Method: salting out / pH: 6 / Details: NaCl, pH 6, SALTING OUT, temperature 295K |
-Data collection
Diffraction | Mean temperature: 295 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID31 / Wavelength: 0.700667 Å |
Detector | Type: CUSTOM-MADE / Detector: DIFFRACTOMETER / Date: Dec 3, 2003 Details: DOUBLE SI(111) MONOCHROMATOR, 9 CHANNEL SI(111) MULTI-ANALYSER |
Radiation | Monochromator: DOUBLE SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.700667 Å / Relative weight: 1 |
Reflection | Resolution: 3.35→95.1 Å / Num. all: 2099 / Num. obs: 2099 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TEW Resolution: 3.35→95.1 Å / Isotropic thermal model: OVERALL / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: POWDER DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.69 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.35→95.1 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|