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Yorodumi- PDB-1ovt: REFINED CRYSTALLOGRAPHIC STRUCTURE OF HEN OVOTRANSFERRIN AT 2.4 A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ovt | ||||||
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Title | REFINED CRYSTALLOGRAPHIC STRUCTURE OF HEN OVOTRANSFERRIN AT 2.4 ANGSTROMS RESOLUTION | ||||||
Components | OVOTRANSFERRIN | ||||||
Keywords | IRON TRANSPORT PROTEIN | ||||||
Function / homology | Function and homology information extracellular sequestering of iron ion / organomineral extracellular matrix / antimicrobial humoral response / intracellular sequestering of iron ion / ferric iron binding / acute-phase response / recycling endosome / antibacterial humoral response / iron ion transport / response to lipopolysaccharide ...extracellular sequestering of iron ion / organomineral extracellular matrix / antimicrobial humoral response / intracellular sequestering of iron ion / ferric iron binding / acute-phase response / recycling endosome / antibacterial humoral response / iron ion transport / response to lipopolysaccharide / early endosome / response to xenobiotic stimulus / iron ion binding / extracellular space / plasma membrane Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.4 Å | ||||||
Authors | Kurokawa, H. / Mikami, B. / Hirose, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1995 Title: Crystal structure of diferric hen ovotransferrin at 2.4 A resolution. Authors: Kurokawa, H. / Mikami, B. / Hirose, M. #1: Journal: Biochemistry / Year: 1993 Title: Structural Evidence for a Ph Sensitive Di-Lysine Trigger in the Hen Ovotransferrin N-Lobe: Implications for Transferrin Iron Release Authors: Dewan, J.C. / Mikami, B. / Hirose, M. / Sacchettini, J.C. #2: Journal: J.Biochem.(Tokyo) / Year: 1990 Title: Crystallization of N-Terminal Lobe of Ovotransferrin Authors: Mikami, B. / Hirose, M. | ||||||
History |
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Remark 700 | SHEET THERE IS ONE BIFURCATED SHEET IN EACH OF THE TWO LOBES OF OVOTRANSFERRIN. SHEET S1 IS ...SHEET THERE IS ONE BIFURCATED SHEET IN EACH OF THE TWO LOBES OF OVOTRANSFERRIN. SHEET S1 IS PRESENTED AS SHEETS S1A, S1B, AND S1C ON SHEET RECORDS BELOW. NOTE THAT STRANDS 4 OF S1A AND 3 OF S1B ARE IDENTICAL, STRANDS 1 OF S1B AND 3 OF S1C ARE IDENTICAL, AND STRANDS 2 OF S1B AND 4 OF S1C ARE IDENTICAL. SHEET S2 IS PRESENTED AS SHEETS S2A, S2B, AND S2C ON SHEET RECORDS BELOW. NOTE THAT STRANDS 4 OF S2A AND 3 OF S2B ARE IDENTICAL, STRANDS 1 OF S2B AND 3 OF S2C ARE IDENTICAL, AND STRANDS 2 OF S2B AND 4 OF S2C ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ovt.cif.gz | 141.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ovt.ent.gz | 115.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ovt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/1ovt ftp://data.pdbj.org/pub/pdb/validation_reports/ov/1ovt | 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: CIS PROLINE - PRO 71 / 2: CIS PROLINE - PRO 287 3: SER 339 - PRO 340 OMEGA = 143.08 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 4: ARG 427 - PRO 428 OMEGA = 238.29 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 5: PRO 509 - PRO 510 OMEGA = 250.41 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION |
-Components
#1: Protein | Mass: 75929.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DIFERRIC FORM / Source: (natural) Gallus gallus (chicken) / References: UniProt: P02789 | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.94 % | ||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5.9 / Method: batch method | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Detector | Date: Dec 3, 1993 |
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Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 28473 / % possible obs: 87 % / Redundancy: 3.2 % |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 11 Å / Observed criterion σ(F): 2 / Num. measured all: 61204 |
-Processing
Software |
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Refinement | Resolution: 2.4→11 Å / σ(F): 2 /
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Displacement parameters | Biso mean: 24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→11 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.265 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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