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Yorodumi- PDB-1rcm: CRYSTAL STRUCTURE OF A UBIQUITIN-DEPENDENT DEGRADATION SUBSTRATE:... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rcm | ||||||
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Title | CRYSTAL STRUCTURE OF A UBIQUITIN-DEPENDENT DEGRADATION SUBSTRATE: A THREE-DISULFIDE FORM OF LYSOZYME | ||||||
Components | HEN EGG WHITE LYSOZYME | ||||||
Keywords | HYDROLASE(O-GLYCOSYL) | ||||||
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 | X-RAY DIFFRACTION / Resolution: 1.9 Å | ||||||
Authors | Hill, C.P. / Johnston, N.L. / Cohen, R.E. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1993 Title: Crystal structure of a ubiquitin-dependent degradation substrate: a three-disulfide form of lysozyme. Authors: Hill, C.P. / Johnston, N.L. / Cohen, R.E. #1: Journal: J.Biol.Chem. / Year: 1991 Title: Specific Disulfide Cleavage is Required for Ubiquitin Conjugation and Degradation of Lysozyme Authors: Dunten, R.L. / Cohen, R.E. / Gregori, L. / Chau, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rcm.cif.gz | 59.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rcm.ent.gz | 47.7 KB | Display | PDB format |
PDBx/mmJSON format | 1rcm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rcm_validation.pdf.gz | 429.4 KB | Display | wwPDB validaton report |
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Full document | 1rcm_full_validation.pdf.gz | 434.8 KB | Display | |
Data in XML | 1rcm_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 1rcm_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/1rcm ftp://data.pdbj.org/pub/pdb/validation_reports/rc/1rcm | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Atom site foot note | 1: RESIDUES CYS A 127 AND CYS B 127 ARE CARBOXYMETHYLATED. |
-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.25 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 3.8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 10 Å / Num. obs: 18295 / % possible obs: 93.8 % / Rmerge F obs: 0.185 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.185 / Rfactor obs: 0.185 / Highest resolution: 1.9 Å Details: THE DISULFIDE BETWEEN RESIDUES 6 AND 127 HAS BEEN REDUCED AND CARBOXYMETHYLATED. THE CARBOXYMETHYL GROUP BOUND TO CYS 6 COULD NOT BE LOCATED DURING THE CRYSTALLOGRAPHIC ANALYSIS AND IS NOT ...Details: THE DISULFIDE BETWEEN RESIDUES 6 AND 127 HAS BEEN REDUCED AND CARBOXYMETHYLATED. THE CARBOXYMETHYL GROUP BOUND TO CYS 6 COULD NOT BE LOCATED DURING THE CRYSTALLOGRAPHIC ANALYSIS AND IS NOT INCLUDED IN THE COORDINATE FILE. THE CARBOXYMETHYL GROUP BOUND TO CYS 127 IS PRESENTED AS HET GROUP ACT 127 AT THE END OF THE CHAIN. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.9 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.9 Å / Rfactor obs: 0.185 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.8 |