+Open data
-Basic information
Entry | Database: PDB / ID: 1nol | ||||||
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Title | OXYGENATED HEMOCYANIN (SUBUNIT TYPE II) | ||||||
Components | HEMOCYANIN (SUBUNIT TYPE II) | ||||||
Keywords | OXYGEN TRANSPORT | ||||||
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 | Hazes, B. / Hol, W.G.J. | ||||||
Citation | Journal: Protein Sci. / Year: 1993 Title: Crystal structure of deoxygenated Limulus polyphemus subunit II hemocyanin at 2.18 A resolution: clues for a mechanism for allosteric regulation. Authors: Hazes, B. / Magnus, K.A. / Bonaventura, C. / Bonaventura, J. / Dauter, Z. / Kalk, K.H. / Hol, W.G. #1: Journal: J.Mol.Biol. / Year: 1989 Title: Crystal Structure of Hexameric Haemocyanin from Panulirus Interruptus Refined at 3.2 Angstroms Resolution Authors: Volbeda, A. / Hol, W.G.J. #2: Journal: J.Biol.Chem. / Year: 1986 Title: Structure of Hemocyanin II from the Horseshoe Crab, Limulus Polyphemus Authors: Nakashima, H. / Behrens, P.Q. / Moore, M.D. / Yokota, E. / Riggs, A.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nol.cif.gz | 136.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nol.ent.gz | 110.4 KB | Display | PDB format |
PDBx/mmJSON format | 1nol.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/1nol ftp://data.pdbj.org/pub/pdb/validation_reports/no/1nol | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: GLU 309 - SER 310 OMEGA = 356.79 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: GLY 525 - LEU 526 OMEGA = 113.53 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 3: CIS PROLINE - PRO 599 | ||||||||
Details | BIOLOGICAL UNIT THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. APPLIED TO RESIDUES: 1 .. 633 A HEMOCYANIN HEXAMER IS OBTAINED BY APPLYING THE CRYSTALLOGRAPHIC SYMMETRY OPERATORS. HOWEVER, ONE SHOULD REMEMBER THAT IN THE BIOLOGICAL MOLECULE THERE ARE 8 OF THESE HEXAMERS AND THAT EACH HEXAMER CONSISTS OF SEVERAL CHAINS WITH RELATED BUT DIFFERENT AMINO ACID SEQUENCES. SYMMETRY1 1 0.000000 0.000000 1.000000 0.00000 SYMMETRY2 1 1.000000 0.000000 0.000000 0.00000 SYMMETRY3 1 0.000000 1.000000 0.000000 0.00000 SYMMETRY1 2 0.000000 1.000000 0.000000 0.00000 SYMMETRY2 2 0.000000 0.000000 1.000000 0.00000 SYMMETRY3 2 1.000000 0.000000 0.000000 0.00000 SYMMETRY1 3 0.000000 -1.000000 0.000000 0.00000 SYMMETRY2 3 -1.000000 0.000000 0.000000 0.00000 SYMMETRY3 3 0.000000 0.000000 -1.000000 0.00000 SYMMETRY1 4 -1.000000 0.000000 0.000000 0.00000 SYMMETRY2 4 0.000000 0.000000 -1.000000 0.00000 SYMMETRY3 4 0.000000 -1.000000 0.000000 0.00000 SYMMETRY1 5 0.000000 0.000000 -1.000000 0.00000 SYMMETRY2 5 0.000000 -1.000000 0.000000 0.00000 SYMMETRY3 5 -1.000000 0.000000 0.000000 0.00000 |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 72757.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Limulus polyphemus (Atlantic horseshoe crab) Tissue: HEMOLYMPH / References: UniProt: P04253 |
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-Non-polymers , 5 types, 217 molecules
#2: Chemical | #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-NO3 / | #5: Chemical | ChemComp-PER / | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | THE STRUCTURE IS BELIEVED TO REPRESENT AN OXYGENATED |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.59 % |
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Crystal grow | PH range: 6.5-7.0 |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Wavelength: 1.5418 Å |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→33.8 Å / Num. obs: 24861 / % possible obs: 83.7 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.052 |
-Processing
Software |
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Refinement | Resolution: 2.4→8 Å / σ(F): 0 Details: THE NON-STANDARD RHOMBOHEDRAL SETTING OF R 3 2 WAS USED.
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Displacement parameters | Biso mean: 16.67 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
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Refine LS restraints |
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