- PDB-1sqy: Structure of human diferric lactoferrin at 2.5A resolution using ... -
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Open data
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Basic information
Entry
Database: PDB / ID: 1sqy
Title
Structure of human diferric lactoferrin at 2.5A resolution using crystals grown at pH 6.5
Components
lactoferrin
Keywords
METAL BINDING PROTEIN / HUMAN DIFERRIC / LACTOFERRIN / pH 6.5
Function / homology
Function and homology information
negative regulation by host of viral process / membrane destabilizing activity / Mtb iron assimilation by chelation / phagocytic vesicle lumen / positive regulation of toll-like receptor 4 signaling pathway / Metal sequestration by antimicrobial proteins / negative regulation of viral process / negative regulation of cysteine-type endopeptidase activity / negative regulation of tumor necrosis factor (ligand) superfamily member 11 production / negative regulation of single-species biofilm formation in or on host organism ...negative regulation by host of viral process / membrane destabilizing activity / Mtb iron assimilation by chelation / phagocytic vesicle lumen / positive regulation of toll-like receptor 4 signaling pathway / Metal sequestration by antimicrobial proteins / negative regulation of viral process / negative regulation of cysteine-type endopeptidase activity / negative regulation of tumor necrosis factor (ligand) superfamily member 11 production / negative regulation of single-species biofilm formation in or on host organism / positive regulation of bone mineralization involved in bone maturation / negative regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of osteoclast development / specific granule / antifungal humoral response / positive regulation of chondrocyte proliferation / negative regulation of ATP-dependent activity / regulation of tumor necrosis factor production / bone morphogenesis / Antimicrobial peptides / cysteine-type endopeptidase inhibitor activity / negative regulation of viral genome replication / positive regulation of osteoblast proliferation / humoral immune response / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of osteoblast differentiation / ossification / regulation of cytokine production / protein serine/threonine kinase activator activity / innate immune response in mucosa / secretory granule / lipopolysaccharide binding / positive regulation of protein serine/threonine kinase activity / recycling endosome / specific granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / tertiary granule lumen / positive regulation of NF-kappaB transcription factor activity / heparin binding / positive regulation of canonical NF-kappaB signal transduction / iron ion transport / antibacterial humoral response / defense response to Gram-negative bacterium / killing of cells of another organism / early endosome / iron ion binding / Amyloid fiber formation / serine-type endopeptidase activity / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / protein-containing complex / proteolysis / DNA binding / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane / cytoplasm Similarity search - Function
Resolution: 2.5→19.73 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.941 / SU B: 12.477 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R: 0.505 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21517
1539
5.1 %
RANDOM
Rwork
0.20381
-
-
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all
0.22
30468
-
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obs
0.2044
28929
100 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 48.154 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.61 Å2
0 Å2
0 Å2
2-
-
1.13 Å2
0 Å2
3-
-
-
-2.74 Å2
Refine analyze
Luzzati coordinate error obs: 0.32 Å
Refinement step
Cycle: LAST / Resolution: 2.5→19.73 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5347
0
66
306
5719
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.021
5543
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
4883
X-RAY DIFFRACTION
r_angle_refined_deg
1.728
1.968
7512
X-RAY DIFFRACTION
r_angle_other_deg
1.125
3
11374
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
2.304
3
690
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
19.075
15
950
X-RAY DIFFRACTION
r_chiral_restr
0.118
0.2
809
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
6215
X-RAY DIFFRACTION
r_gen_planes_other
0.003
0.02
1141
X-RAY DIFFRACTION
r_nbd_refined
0.256
0.3
1374
X-RAY DIFFRACTION
r_nbd_other
0.24
0.3
4897
X-RAY DIFFRACTION
r_nbtor_other
0.472
0.5
4
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.157
0.5
424
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.108
0.5
12
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.243
0.3
7
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.228
0.3
19
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.198
0.5
5
X-RAY DIFFRACTION
r_symmetry_hbond_other
0.139
0.5
1
X-RAY DIFFRACTION
r_mcbond_it
0.884
1.5
3442
X-RAY DIFFRACTION
r_mcangle_it
1.675
2
5502
X-RAY DIFFRACTION
r_scbond_it
2.19
3
2101
X-RAY DIFFRACTION
r_scangle_it
3.742
4.5
2010
LS refinement shell
Resolution: 2.5→2.564 Å / Total num. of bins used: 20 /
Rfactor
Num. reflection
Rfree
0.345
111
Rwork
0.304
2067
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