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Yorodumi- PDB-1dot: CRYSTALLOGRAPHIC STRUCTURE OF DUCK OVOTRANSFERRIN AT 2.3 ANGSTROM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dot | ||||||
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Title | CRYSTALLOGRAPHIC STRUCTURE OF DUCK OVOTRANSFERRIN AT 2.3 ANGSTROMS RESOLUTION | ||||||
Components | DUCK OVOTRANSFERRIN | ||||||
Keywords | IRON TRANSPORT PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Anas platyrhynchos (mallard) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 Å | ||||||
Authors | Rawas, A. / Muirhead, H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Structure of diferric duck ovotransferrin at 2.35 A resolution. Authors: Rawas, A. / Muirhead, H. / Williams, J. #1: Journal: J.Mol.Biol. / Year: 1989 Title: Preliminary Crystallographic Studies on Duck Ovotransferrin Authors: Rawas, A. / Moreton, K. / Muirhead, H. / Williams, J. #2: Journal: Biochemistry / Year: 1988 Title: Molecular Structure of Serum Transferrin at 3.3 Angstroms Resolution Authors: Bailey, S. / Evans, R.W. / Garratt, R.C. / Gorinsky, B. / Hasnain, S. / Horsburgh, C. / Jhoti, H. / Lindley, P.F. / Mydin, A. / Sarra, R. / Watson, J.L. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987 Title: Structure of Human Lactoferrin at 3.2 Angstroms Resolution Authors: Anderson, B.F. / Baker, H.M. / Dodson, E.J. / Norris, G.E. / Rumball, S.V. / Waters, J.M. / Baker, E.N. | ||||||
History |
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Remark 700 | SHEET SHEETS N1, N2, C1, AND C2 ARE MIXED BETA SHEETS. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dot.cif.gz | 154.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dot.ent.gz | 118.2 KB | Display | PDB format |
PDBx/mmJSON format | 1dot.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/1dot ftp://data.pdbj.org/pub/pdb/validation_reports/do/1dot | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: PRO 2 - PRO 3 OMEGA = 149.33 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: PRO 3 - LYS 4 OMEGA = 132.22 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 3: CIS PROLINE - PRO 71 4: THR 279 - SER 280 OMEGA = 300.70 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 5: LYS 344 - ILE 345 OMEGA = 127.92 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 75731.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Anas platyrhynchos (mallard) / Cellular location: EGG WHITE / References: UniProt: P56410 |
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-Sugars , 2 types, 3 molecules
#2: Sugar | #3: Sugar | ChemComp-FUC / | |
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-Non-polymers , 3 types, 322 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.88 % | ||||||||||||||||||||
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Crystal | *PLUS Density % sol: 48 % | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K / pH: 5.8 / Method: batch method | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 |
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Detector | Detector: FILM / Date: 1986 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Num. obs: 29846 / % possible obs: 90 % / Rmerge(I) obs: 0.059 |
Reflection | *PLUS Highest resolution: 2.35 Å / Lowest resolution: 10 Å / Rmerge(I) obs: 0.059 |
-Processing
Software |
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Refinement | Resolution: 2.35→10 Å / σ(F): 1
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Displacement parameters | Biso mean: 28.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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