[English] 日本語
Yorodumi- PDB-1oxy: CRYSTALLOGRAPHIC ANALYSIS OF OXYGENATED AND DEOXYGENATED STATES O... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oxy | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTALLOGRAPHIC ANALYSIS OF OXYGENATED AND DEOXYGENATED STATES OF ARTHROPOD HEMOCYANIN SHOWS UNUSUAL DIFFERENCES | ||||||
Components | HEMOCYANIN (SUBUNIT TYPE II) | ||||||
Keywords | OXYGEN TRANSPORT / HEMOCYANIN / COPPER PROTEIN | ||||||
Function / homology | Function and homology information chloride ion binding / oxygen transport / oxygen carrier activity / oxidoreductase activity / copper ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Limulus polyphemus (Atlantic horseshoe crab) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.4 Å | ||||||
Authors | Ton-that, H. / Magnus, K. | ||||||
Citation | Journal: Proteins / Year: 1994 Title: Crystallographic analysis of oxygenated and deoxygenated states of arthropod hemocyanin shows unusual differences. Authors: Magnus, K.A. / Hazes, B. / Ton-That, H. / Bonaventura, C. / Bonaventura, J. / Hol, W.G. #1: Journal: Proteins / Year: 1991 Title: Hexamers of Subunit II from Limulus Hemocyanin (A 48mer) Have the Same Quaternary Structure as Whole Panulirus Hemocyanin Molecules Authors: Magnus, K.A. / Lattman, E.E. / Volbeda, A. / Hol, W.G.L. #2: Journal: J.Mol.Biol. / Year: 1977 Title: Crystals of a Functional 70,000 Molecular Weight Subunit of Hemocyanin from Limulus Polyphemus Authors: Magnus, K.A. / Love, W.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1oxy.cif.gz | 132.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1oxy.ent.gz | 107.5 KB | Display | PDB format |
PDBx/mmJSON format | 1oxy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/1oxy ftp://data.pdbj.org/pub/pdb/validation_reports/ox/1oxy | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: PHE 388 - PRO 389 OMEGA = 218.97 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: CIS PROLINE - PRO 599 |
-Components
#1: Protein | Mass: 72657.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Limulus polyphemus (Atlantic horseshoe crab) References: UniProt: P04253 | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-OXY / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.7 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 6.2 / Method: unknown | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 32972 / % possible obs: 81 % / Observed criterion σ(I): 2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.4→6 Å / σ(F): 2 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.37 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|