- PDB-4ap6: Crystal structure of human POFUT2 E54A mutant in complex with GDP... -
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Basic information
Entry
Database: PDB / ID: 4ap6
Title
Crystal structure of human POFUT2 E54A mutant in complex with GDP- fucose
Components
GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 2
Keywords
TRANSFERASE / GT-B / GT68
Function / homology
Function and homology information
positive regulation of protein folding / peptide-O-fucosyltransferase / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / regulation of secretion / O-glycosylation of TSR domain-containing proteins / fucose metabolic process / regulation of epithelial to mesenchymal transition / mesoderm formation / regulation of gene expression ...positive regulation of protein folding / peptide-O-fucosyltransferase / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / regulation of secretion / O-glycosylation of TSR domain-containing proteins / fucose metabolic process / regulation of epithelial to mesenchymal transition / mesoderm formation / regulation of gene expression / endoplasmic reticulum membrane / Golgi apparatus Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Compound details
ENGINEERED RESIDUE IN CHAIN A, GLU 54 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 54 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, GLU 54 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 54 TO ALA ENGINEERED RESIDUE IN CHAIN C, GLU 54 TO ALA ENGINEERED RESIDUE IN CHAIN D, GLU 54 TO ALA
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 3.2 Å3/Da / Density % sol: 63 % / Description: NONE
Monochromator: DUAL CHANNEL CUT CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 3.4→40 Å / Num. obs: 32751 / % possible obs: 93.3 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 77.22 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 11
Reflection shell
Resolution: 3.4→3.63 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.1 / % possible all: 93.6
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Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE: 1.7.1_743)
refinement
XDS
datareduction
XSCALE
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.401→39.686 Å / SU ML: 0.89 / σ(F): 1.99 / Phase error: 22 / Stereochemistry target values: ML Details: RESIDUES 298-302 ARE PARTIALLY DISORDERED. CHAIN D IS EITHER HIGHLY MOBILE OR NOT FULLY OCCUPIED IN THE CRYSTAL.
Rfactor
Num. reflection
% reflection
Rfree
0.238
1622
4.9 %
Rwork
0.1924
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-
obs
0.1947
32745
93.55 %
Solvent computation
Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.003 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
2.2146 Å2
0 Å2
0 Å2
2-
-
2.2146 Å2
0 Å2
3-
-
-
-4.4293 Å2
Refinement step
Cycle: LAST / Resolution: 3.401→39.686 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
12974
0
240
8
13222
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.011
13605
X-RAY DIFFRACTION
f_angle_d
1.292
18456
X-RAY DIFFRACTION
f_dihedral_angle_d
18.276
5068
X-RAY DIFFRACTION
f_chiral_restr
0.094
1919
X-RAY DIFFRACTION
f_plane_restr
0.006
2331
Refine LS restraints NCS
Ens-ID
Dom-ID
Auth asym-ID
Number
Refine-ID
Type
Rms dev position (Å)
1
1
A
3085
X-RAY DIFFRACTION
POSITIONAL
1
2
B
3085
X-RAY DIFFRACTION
POSITIONAL
0.054
1
3
C
3085
X-RAY DIFFRACTION
POSITIONAL
0.06
1
4
D
3085
X-RAY DIFFRACTION
POSITIONAL
0.05
2
1
A
38
X-RAY DIFFRACTION
POSITIONAL
2
2
B
38
X-RAY DIFFRACTION
POSITIONAL
0.028
2
3
C
38
X-RAY DIFFRACTION
POSITIONAL
0.031
2
4
D
38
X-RAY DIFFRACTION
POSITIONAL
0.034
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
3.4014-3.5015
0.2949
132
0.2853
2499
X-RAY DIFFRACTION
93
3.5015-3.6144
0.3169
106
0.2648
2675
X-RAY DIFFRACTION
96
3.6144-3.7435
0.3107
139
0.2476
2613
X-RAY DIFFRACTION
96
3.7435-3.8932
0.2991
140
0.2357
2605
X-RAY DIFFRACTION
95
3.8932-4.0703
0.2635
140
0.207
2600
X-RAY DIFFRACTION
95
4.0703-4.2846
0.2591
138
0.1766
2602
X-RAY DIFFRACTION
95
4.2846-4.5527
0.1977
142
0.1605
2604
X-RAY DIFFRACTION
94
4.5527-4.9036
0.2
139
0.1428
2606
X-RAY DIFFRACTION
94
4.9036-5.396
0.2021
131
0.1604
2565
X-RAY DIFFRACTION
93
5.396-6.1743
0.2261
140
0.1877
2596
X-RAY DIFFRACTION
92
6.1743-7.7694
0.2338
139
0.1827
2562
X-RAY DIFFRACTION
91
7.7694-39.6887
0.2044
136
0.1786
2596
X-RAY DIFFRACTION
89
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
2.2242
0.0895
-0.4312
4.3319
0.6776
4.9894
-0.1793
0.1207
0.1836
-0.197
0.2317
-0.3
-0.4841
0.3695
-0.0192
0.6263
-0.2184
0.1412
0.6814
-0.1797
0.7199
18.6794
9.0046
15.6273
2
2.9722
1.354
0.7231
6.2079
0.2072
2.7025
-0.146
0.2812
-0.259
-0.4576
0.3217
-0.7922
-0.001
0.5069
-0.1085
0.5378
-0.0173
0.212
0.7703
-0.3067
0.7786
21.1672
-18.0963
5.0223
3
5.3518
-0.596
0.0219
2.4709
-0.0709
3.4902
0.1791
-0.0242
-0.0905
-0.162
-0.0984
-0.0094
-0.0785
-0.3305
-0.0672
0.557
0.1261
0.062
0.4266
-0.0388
0.3733
-13.0105
-44.6988
-13.7788
4
4.8163
-0.6917
-0.9928
5.8506
-0.8652
4.6945
0.1147
-0.5085
-0.4455
0.1546
-0.0322
-0.3807
0.124
0.2107
-0.1201
0.3527
0.064
-0.1004
0.6128
-0.0318
0.4737
5.0856
-52.2743
7.8356
5
3.7079
0.2823
0.7342
5.2068
-0.2335
3.5725
0.1091
0.1597
-0.3281
-0.1478
0.1144
0.4661
0.2648
-0.3462
-0.1684
0.5799
-0.0831
-0.2214
0.8947
0.1262
0.5168
12.7115
-94.7244
26.73
6
7.4011
-0.017
-0.7287
3.334
-0.0004
7.806
0.0584
-0.1932
0.1515
0.5613
0.1542
0.4838
-0.5589
-0.2936
-0.1943
0.7793
0.0384
-0.0079
0.5837
0.1603
0.6647
4.5596
-70.7244
41.4416
7
4.5927
0.416
1.0882
3.7135
-1.3778
1.5651
-0.4297
-0.3778
0.8553
0.6298
0.3294
-0.3923
-1.81
0.0336
0.0945
2.41
-0.2016
0.1715
0.7628
-0.0056
1.2445
0.1885
-63.9141
88.3988
8
4.0644
1.6748
0.496
7.7212
-0.7244
2.3087
-0.2883
0.1344
1.0597
-0.5994
0.3393
1.078
-1.8181
-0.6786
-0.0967
2.1274
0.3558
0.0866
1.0248
0.3108
1.3195
-21.4435
-60.6289
69.0557
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAINAAND (RESSEQ41:243)
2
X-RAY DIFFRACTION
2
CHAINAAND (RESSEQ244:429)
3
X-RAY DIFFRACTION
3
CHAINBAND (RESSEQ41:243)
4
X-RAY DIFFRACTION
4
CHAINBAND (RESSEQ244:429)
5
X-RAY DIFFRACTION
5
CHAINCAND (RESSEQ41:243)
6
X-RAY DIFFRACTION
6
CHAINCAND (RESSEQ244:429)
7
X-RAY DIFFRACTION
7
CHAINDAND (RESSEQ41:243)
8
X-RAY DIFFRACTION
8
CHAINDAND (RESSEQ244:429)
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