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Yorodumi- PDB-1ja2: BINDING OF N-ACETYLGLUCOSAMINE TO CHICKEN EGG LYSOZYME: A POWDER ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ja2 | ||||||
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Title | BINDING OF N-ACETYLGLUCOSAMINE TO CHICKEN EGG LYSOZYME: A POWDER DIFFRACTION STUDY | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE / POWDER DIFFRACTION / RIETVELD REFINEMENT / LYSOZYME | ||||||
Function / homology | Function and homology information Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / 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 ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / 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 / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | POWDER DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å | ||||||
Authors | Von Dreele, R.B. | ||||||
Citation | 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. #1: Journal: J.Appl.Crystallogr. / Year: 1999 Title: Combined Rietveld and Stereochemical Restraint Refinement of a Protein Crystal Structure Authors: Von Dreele, R.B. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: The First Protein Crystal Structure Determined from Resolution X-Ray Powder Diffraction Data: A Variant of the T3R3 Human Insulin Zinc Complex Produced by Grinding Authors: Von Dreele, R.B. / Stephens, P.W. / Blessing, R.H. / Smith, G.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ja2.cif.gz | 33.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ja2.ent.gz | 19.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ja2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ja2_validation.pdf.gz | 346.3 KB | Display | wwPDB validaton report |
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Full document | 1ja2_full_validation.pdf.gz | 358.3 KB | Display | |
Data in XML | 1ja2_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | 1ja2_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/1ja2 ftp://data.pdbj.org/pub/pdb/validation_reports/ja/1ja2 | HTTPS FTP |
-Related structure data
Related structure data | 1ja4C 1ja6C 1ja7C 1rfpS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P00698, lysozyme |
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-Experimental details
-Experiment
Experiment | Method: POWDER DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.68 % |
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Crystal grow | Temperature: 296 K / Method: precipitation / pH: 4.8 Details: rapid precipitation from 0.5M NACL IN PH 5.0 0.05M KHPHTHALATE/NAOH BUFFER, at 296K, pH 4.8 |
Crystal grow | *PLUS Method: unknown / Details: Von Dreele, R.B., (2000) Acta Cryst., D56, 1549. |
Components of the solutions | *PLUS Conc.: 1.0 M / Chemical formula: NaCl |
-Data collection
Diffraction | Mean temperature: 296 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X3B1 / Wavelength: 0.70003 Å |
Detector | Detector: SCINTILLATOR / Date: Oct 23, 2000 / Details: 2MM X 8MM BEAM |
Radiation | Monochromator: DOUBLE SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
Radiation wavelength | Wavelength: 0.70003 Å / Relative weight: 1 |
Reflection | Resolution: 2.87→40.03 Å / Num. all: 3112 / Num. obs: 3112 / % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RFP Resolution: 2.87→40.03 Å / Isotropic thermal model: Overall fixed / Stereochemistry target values: Engh & Huber Details: Used band matrix least squares, band width 300 parameters
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Displacement parameters | Biso mean: 23.7 Å2 | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.87→40.03 Å
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Refine LS restraints |
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