- PDB-1ryx: Crystal structure of hen serum transferrin in apo- form -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1ryx
Title
Crystal structure of hen serum transferrin in apo- form
Components
Ovotransferrin
Keywords
METAL TRANSPORT / Hen serum transferrin / Apo- form / Domain Orientation
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 / iron ion transport / antibacterial humoral response / 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 / iron ion transport / antibacterial humoral response / response to lipopolysaccharide / early endosome / response to xenobiotic stimulus / iron ion binding / extracellular space / plasma membrane Similarity search - Function
Resolution: 3.5→19.69 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 4475883.76 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: THE RESIDUES WHOSE SIDE CHAINS COULD NOT BE LOCATED IN THE ELECTRON DENSITY MAP WERE KEPT AS ALANINE, HOWEVER, THE RESIDUE NAMES REMAIN UNALTERED IN THIS PDB FILE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.341
444
5.2 %
RANDOM
Rwork
0.283
-
-
-
obs
0.283
8604
88.3 %
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Displacement parameters
Biso mean: 21.6 Å2
Baniso -1
Baniso -2
Baniso -3
1-
2.89 Å2
0 Å2
0 Å2
2-
-
2.89 Å2
0 Å2
3-
-
-
-5.78 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.75 Å
0.58 Å
Luzzati d res low
-
20 Å
Luzzati sigma a
0.66 Å
0.42 Å
Refinement step
Cycle: LAST / Resolution: 3.5→19.69 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4657
0
0
0
4657
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
c_bond_d
0.011
X-RAY DIFFRACTION
c_angle_deg
1.9
X-RAY DIFFRACTION
c_dihedral_angle_d
25.2
X-RAY DIFFRACTION
c_improper_angle_d
1.29
LS refinement shell
Resolution: 3.5→3.72 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 6
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