- PDB-4qot: Crystal structure of human copper chaperone bound to the platinum ion -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4qot
Title
Crystal structure of human copper chaperone bound to the platinum ion
Components
Copper transport protein ATOX1
Keywords
CHAPERONE / Metal-binding / Metal transport / platinum / oxaliplatin
Function / homology
Function and homology information
metallochaperone activity / Ion influx/efflux at host-pathogen interface / copper-dependent protein binding / copper chaperone activity / copper ion transport / Detoxification of Reactive Oxygen Species / cuprous ion binding / intracellular copper ion homeostasis / response to oxidative stress / copper ion binding / cytosol Similarity search - Function
Resolution: 2.2→42.49 Å / SU ML: 0.28 / σ(F): 1.35 / Phase error: 26.01 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.239
465
4.82 %
Rwork
0.188
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obs
0.19
9647
99.3 %
all
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9697
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Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 2.2→42.49 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1012
0
27
48
1087
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.008
1077
X-RAY DIFFRACTION
f_angle_d
1.063
1444
X-RAY DIFFRACTION
f_dihedral_angle_d
13.544
400
X-RAY DIFFRACTION
f_chiral_restr
0.076
167
X-RAY DIFFRACTION
f_plane_restr
0.008
176
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.2012-2.5197
0.287
156
0.2429
3026
X-RAY DIFFRACTION
99
2.5197-3.1745
0.2728
169
0.2236
3050
X-RAY DIFFRACTION
100
3.1745-42.4961
0.206
140
0.1604
3106
X-RAY DIFFRACTION
99
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
0.0283
0.1659
0.2118
0.9681
1.2453
1.6118
0.1033
0.1397
-0.0239
-0.1434
-0.0912
0.0525
0.1025
-0.0179
-0.0067
0.3115
-0.0461
-0.0388
0.2318
0.063
0.2162
24.2328
151.454
-34.9802
2
1.4635
0.0344
-0.3366
3.4321
1.5297
2.4523
0.0116
-0.0879
0.1649
0.0072
0.1063
-0.0913
-0.2668
0.2624
-0.1236
0.4844
-0.1155
-0.1849
0.286
-0.1165
0.3927
43.2217
159.6953
-36.0526
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
(chainAandresseq15:15) or (chainAandresseq12:12) or (chainBandresseq15:15) or (chainBandresseq12:12) or (chainAandresseq101:101)
2
X-RAY DIFFRACTION
2
(chainBandresseq5:5andaltloc 'B') or (chainBandresseq101:101) or (chainBandresseq104:104) or (chainBandresseq41:41andaltloc 'A') or (chainBandresseq3:3andaltloc 'A')
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