- PDB-4mj4: Human iduronidase apo structure P21 form -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4mj4
Title
Human iduronidase apo structure P21 form
Components
Alpha-L-iduronidaseIduronidase
Keywords
HYDROLASE / TIM barrel / beta sandwich / fibronectin type III / hydrolyze iduronic acids from the non-reducing ends of glycosaminoglycan / intracellular / lysosomal
Function / homology
Function and homology information
L-iduronidase / L-iduronidase activity / disaccharide metabolic process / MPS I - Hurler syndrome / heparin catabolic process / dermatan sulfate catabolic process / glycosaminoglycan catabolic process / CS/DS degradation / heparan sulfate proteoglycan catabolic process / HS-GAG degradation ...L-iduronidase / L-iduronidase activity / disaccharide metabolic process / MPS I - Hurler syndrome / heparin catabolic process / dermatan sulfate catabolic process / glycosaminoglycan catabolic process / CS/DS degradation / heparan sulfate proteoglycan catabolic process / HS-GAG degradation / lysosomal lumen / signaling receptor binding / extracellular exosome Similarity search - Function
: / Alpha-L-iduronidase C-terminal domain / Glycosyl hydrolase domain; family 39 / : / : / Glycosyl hydrolases family 39 active site. / Glycoside hydrolase, family 39 / Glycosyl hydrolases family 39 / Glycosidases / Glycoside hydrolase superfamily ...: / Alpha-L-iduronidase C-terminal domain / Glycosyl hydrolase domain; family 39 / : / : / Glycosyl hydrolases family 39 active site. / Glycoside hydrolase, family 39 / Glycosyl hydrolases family 39 / Glycosidases / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology
Resolution: 2.172→48.71 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 14.389 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.341 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23952
1536
5.1 %
RANDOM
Rwork
0.20144
-
-
-
all
0.20345
29807
-
-
obs
0.20345
28850
96.79 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 37.707 Å2
Baniso -1
Baniso -2
Baniso -3
1-
2.08 Å2
-0 Å2
1.36 Å2
2-
-
-1.68 Å2
-0 Å2
3-
-
-
-0.45 Å2
Refinement step
Cycle: LAST / Resolution: 2.172→48.71 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4790
0
108
116
5014
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.005
0.019
5063
X-RAY DIFFRACTION
r_angle_refined_deg
1.005
1.974
6923
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.537
5
604
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.464
22.255
235
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.093
15
744
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.083
15
49
X-RAY DIFFRACTION
r_chiral_restr
0.064
0.2
762
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.021
3932
X-RAY DIFFRACTION
r_mcbond_it
0.449
2.143
2416
X-RAY DIFFRACTION
r_mcangle_it
0.803
3.211
3017
X-RAY DIFFRACTION
r_scbond_it
0.601
2.324
2647
X-RAY DIFFRACTION
r_long_range_B_refined
3.483
18.866
7612
LS refinement shell
Resolution: 2.172→2.228 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.329
59
88.9 %
Rwork
0.298
1706
-
obs
-
-
77.58 %
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
1.7977
0.8653
-0.7398
2.6093
-0.7473
1.0299
-0.1046
0.0073
0.0573
0.0367
0.1114
-0.1862
0.0282
0.0304
-0.0068
0.1115
0.0116
-0.0251
0.123
-0.0216
0.0554
64.6687
-17.038
96.6032
2
5.1787
2.4176
-7.2189
3.3537
-1.8271
11.5562
0.081
-0.04
-0.0203
-0.2569
0.0335
-0.3902
-0.1836
0.2333
-0.1145
0.1912
0.0312
0.0612
0.0664
0.0065
0.1476
71.5994
-13.6926
75.8148
3
2.9025
0.8163
-0.0794
1.8092
0.8082
1.9702
0.0386
0.0585
-0.0376
-0.316
0.1556
-0.3193
-0.2885
0.2649
-0.1943
0.1279
-0.0568
0.1156
0.0418
-0.0459
0.1099
83.7752
1.425
80.469
4
2.1696
1.7362
0.4484
2.1417
-0.3716
3.7732
-0.0246
-0.0906
-0.2585
0.0806
0.1451
-0.5934
-0.0666
0.3796
-0.1204
0.1469
-0.0291
-0.0035
0.309
-0.1553
0.3596
88.9692
0.8208
92.7127
5
0.2625
0.4477
-0.1735
2.0518
0.3078
0.7495
0.0758
-0.1379
-0.0396
0.2204
0.0186
-0.4241
0.0261
0.1531
-0.0945
0.089
0.01
-0.0564
0.1613
-0.0501
0.1692
81.1868
-10.2611
98.8873
6
1.7238
-0.572
-0.9009
4.2604
3.8342
5.1171
-0.1252
-0.4218
-0.1417
0.5718
0.1188
-0.0893
0.3561
0.4668
0.0064
0.2257
0.0081
-0.0115
0.1913
-0.0087
0.1903
74.8893
-13.4593
95.6139
7
1.071
0.025
-0.3626
1.0782
-0.0317
1.167
-0.0327
-0.028
-0.0075
-0.0089
0.0805
-0.0936
0.077
-0.0086
-0.0478
0.1091
-0.0048
-0.0112
0.0528
-0.0093
0.0739
63.46
-24.5921
90.6047
8
8.1672
-5.2342
-12.7455
22.7057
4.1375
20.7507
-0.2741
-0.0789
-0.1134
0.2076
0.1187
-0.4215
0.4145
0.0926
0.1554
0.2019
0.0207
-0.1125
0.1222
0.0474
0.5446
73.819
-38.122
75.2317
9
1.0731
-0.0828
-0.3901
1.0954
-0.2518
1.1212
-0.0034
0.0099
-0.1174
-0.0947
0.0197
-0.0268
0.0617
-0.0758
-0.0163
0.1244
-0.0003
-0.0011
0.0272
-0.0059
0.0538
58.3173
-30.1365
85.4556
10
4.2541
2.1866
-7.3645
3.715
-3.7824
12.7522
0.4425
0.2899
0.3749
0.2168
0.1776
0.3245
-0.7483
-0.5071
-0.6201
0.2169
0.0155
-0.0085
0.2
0.0223
0.1986
48.2892
-9.98
79.106
11
2.251
-0.6511
-1.1239
2.4389
0.5381
3.0963
0.115
0.2118
0.1094
-0.4884
0.0396
0.1175
-0.2077
0.0416
-0.1547
0.2067
-0.0094
-0.0277
0.0958
0.0154
0.0686
57.1687
-16.5698
70.0173
12
1.8347
-0.2443
-0.4996
1.2752
0.0763
1.5834
0.0436
0.3147
-0.0924
-0.4271
-0.0132
-0.047
0.1162
-0.1489
-0.0305
0.2243
0.0107
-0.0136
0.1333
-0.0089
0.0824
54.5479
-18.9161
68.8256
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
27 - 63
2
X-RAY DIFFRACTION
2
A
64 - 85
3
X-RAY DIFFRACTION
3
A
86 - 186
4
X-RAY DIFFRACTION
4
A
187 - 231
5
X-RAY DIFFRACTION
5
A
232 - 333
6
X-RAY DIFFRACTION
6
A
334 - 355
7
X-RAY DIFFRACTION
7
A
356 - 484
8
X-RAY DIFFRACTION
8
A
485 - 493
9
X-RAY DIFFRACTION
9
A
494 - 541
10
X-RAY DIFFRACTION
10
A
542 - 554
11
X-RAY DIFFRACTION
11
A
555 - 591
12
X-RAY DIFFRACTION
12
A
592 - 640
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