- PDB-4h0w: Bismuth bound human serum transferrin -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4h0w
Title
Bismuth bound human serum transferrin
Components
Serotransferrin
Keywords
METAL TRANSPORT / BISMUTH / IRON TRANSPORTER
Function / homology
Function and homology information
iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / basal part of cell / positive regulation of cell motility / endocytic vesicle / positive regulation of bone resorption / clathrin-coated pit / positive regulation of phosphorylation / ERK1 and ERK2 cascade ...iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / basal part of cell / positive regulation of cell motility / endocytic vesicle / positive regulation of bone resorption / clathrin-coated pit / positive regulation of phosphorylation / ERK1 and ERK2 cascade / ferric iron binding / osteoclast differentiation / basal plasma membrane / cellular response to iron ion / actin filament organization / Iron uptake and transport / Post-translational protein phosphorylation / clathrin-coated endocytic vesicle membrane / regulation of protein stability / ferrous iron binding / regulation of iron ion transport / HFE-transferrin receptor complex / recycling endosome / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / late endosome / Cargo recognition for clathrin-mediated endocytosis / Platelet degranulation / Clathrin-mediated endocytosis / iron ion transport / antibacterial humoral response / cytoplasmic vesicle / secretory granule lumen / intracellular iron ion homeostasis / vesicle / early endosome / blood microparticle / endosome membrane / apical plasma membrane / endoplasmic reticulum lumen / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / cell surface / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function
Resolution: 2.4→36.95 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.909 / SU B: 17.775 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.256
1485
5.1 %
RANDOM
Rwork
0.194
-
-
-
obs
0.197
29240
99 %
-
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: 49.43 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.02 Å2
0 Å2
0 Å2
2-
-
0.02 Å2
0 Å2
3-
-
-
0 Å2
Refinement step
Cycle: LAST / Resolution: 2.4→36.95 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5266
0
37
130
5433
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.022
5438
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.123
1.963
7361
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.64
5
678
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.15
24.571
245
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.564
15
918
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.803
15
26
X-RAY DIFFRACTION
r_chiral_restr
0.083
0.2
783
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.021
4150
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.534
5
3382
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
2.405
6
5408
X-RAY DIFFRACTION
r_scbond_it
2.168
5
2056
X-RAY DIFFRACTION
r_scangle_it
3.264
7.5
1953
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.4→2.47 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.283
116
-
Rwork
0.231
1960
-
obs
-
-
95.62 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
6.0118
-0.6584
-2.8657
3.447
0.7385
4.5672
0.5178
0.4648
0.6506
-0.3036
0.0162
-0.2545
-0.9286
-0.1804
-0.534
0.3316
0.0325
0.1356
0.1279
0.0608
0.2266
47.5181
16.0621
-9.5276
2
2.2058
-0.0402
-1.0731
3.8339
0.8628
7.2304
0.1574
0.0768
0.2212
-0.2753
0.0011
0.0087
-0.3451
0.172
-0.1585
0.0515
-0.011
0.019
0.1252
0.0468
0.1324
39.93
12.8755
21.4193
3
4.9248
-0.3526
-0.5973
4.5411
-0.2733
4.9341
0.1057
-0.1087
0.3018
-0.0355
-0.016
-0.4825
-0.0546
0.6583
-0.0896
0.0728
0.0262
0.0418
0.241
0.013
0.0935
47.3024
8.1672
23.341
4
7.9371
-1.0075
-4.2461
2.6943
1.488
8.4614
0.0117
-0.2795
0.1219
-0.1077
0.0862
-0.0994
-0.3358
-0.0366
-0.0979
0.181
-0.0033
-0.0375
0.0203
0.0215
0.1036
43.3161
9.651
-0.9529
5
3.0986
0.769
1.4519
2.6088
1.0685
3.3516
0.2535
-0.2769
-0.2183
0.2117
-0.1645
-0.0242
0.1847
-0.1088
-0.0889
0.1151
-0.0825
-0.0705
0.1662
0.0597
0.1325
12.9146
-11.1972
-5.9202
6
28.8906
3.5349
8.446
8.8256
2.6292
9.9756
0.5397
-1.5047
-0.2178
0.1589
-0.3825
1.7061
0.1063
-1.0939
-0.1572
0.5325
-0.1935
0.0375
0.6395
-0.0398
0.4597
4.1365
-0.4041
11.4392
7
6.9831
1.3655
0.6825
3.3651
0.8571
0.2397
0.487
-0.5122
-0.688
0.4949
-0.3023
-0.5169
0.3764
-0.1459
-0.1848
0.6291
-0.1747
-0.1788
0.3221
0.0776
0.1406
22.0428
-9.7074
3.8877
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 85
2
X-RAY DIFFRACTION
2
A
86 - 157
3
X-RAY DIFFRACTION
3
A
158 - 244
4
X-RAY DIFFRACTION
4
A
245 - 339
5
X-RAY DIFFRACTION
5
A
340 - 590
6
X-RAY DIFFRACTION
6
A
591 - 625
7
X-RAY DIFFRACTION
7
A
626 - 679
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