- PDB-4mj2: Crystal structure of apo-iduronidase in the R3 form -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4mj2
Title
Crystal structure of apo-iduronidase in the R3 form
Components
Alpha-L-iduronidase
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: 2.1→2.154 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.868 / Mean I/σ(I) obs: 2.33 / % possible all: 95.32
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Processing
Software
Name
Version
Classification
MxDC
datacollection
PHENIX
modelbuilding
REFMAC
5.7.0029
refinement
XDS
datareduction
XDS
datascaling
PHENIX
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.1→49.01 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.946 / SU B: 9.493 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.20637
5233
5 %
RANDOM
Rwork
0.1914
-
-
-
all
0.19215
-
-
-
obs
0.19215
99410
99.54 %
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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: 36.056 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.84 Å2
-1.84 Å2
0 Å2
2-
-
-1.84 Å2
0 Å2
3-
-
-
5.97 Å2
Refinement step
Cycle: LAST / Resolution: 2.1→49.01 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
9551
0
307
433
10291
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.005
0.019
10210
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
9479
X-RAY DIFFRACTION
r_angle_refined_deg
1.006
1.984
13967
X-RAY DIFFRACTION
r_angle_other_deg
0.708
3
21678
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.767
5
1204
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.145
22.206
467
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.433
15
1482
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.497
15
98
X-RAY DIFFRACTION
r_chiral_restr
0.057
0.2
1555
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.021
11370
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
2472
LS refinement shell
Resolution: 2.1→2.154 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.303
371
-
Rwork
0.294
7036
-
obs
-
-
95.32 %
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
0.5234
0.3486
-0.1795
1.9176
-0.138
0.3869
0.0624
-0.0626
0.1316
0.1534
-0.0945
-0.0687
-0.2401
0.1774
0.0321
0.2591
-0.0942
0.0058
0.202
0.0077
0.0973
-118.6783
315.9176
14.0956
2
7.5595
4.1547
4.1396
3.5938
2.1037
2.3158
0.0024
0.0421
0.0936
-0.0607
-0.0099
0.374
-0.0819
0.0485
0.0075
0.3199
-0.0284
0.0006
0.1302
0.0243
0.1527
-140.4011
306.2242
9.7568
3
1.6267
-0.6746
0.7164
1.4059
-1.3205
1.2619
0.0354
0.0598
-0.0675
0.0814
0.0956
0.1939
-0.0361
-0.0724
-0.131
0.1618
-0.0199
0.0417
0.1153
0.0179
0.2473
-145.1533
315.1826
0.6754
4
1.0039
-0.0769
-0.734
1.0705
-0.2039
0.6967
0.015
0.0407
-0.0626
0.0046
0.0388
0.2417
0.0411
0.0095
-0.0539
0.1375
-0.0156
-0.0191
0.1188
-0.0004
0.2017
-143.3848
322.879
-7.0513
5
1.7117
-0.346
-0.9573
1.9046
0.892
2.3084
0.0255
0.112
-0.2238
0.0066
-0.0881
0.152
0.0747
0.0037
0.0625
0.1557
0.0039
-0.021
0.157
0.0162
0.1592
-138.0809
325.3173
-11.6534
6
0.3443
0.0575
0.1258
0.6324
-0.3843
0.3117
0.0462
0.015
-0.005
-0.0075
-0.0682
-0.0309
0.0151
0.0649
0.022
0.182
-0.0083
-0.0043
0.1684
0.0051
0.094
-122.5031
318.9311
-4.3557
7
0.3515
0.744
-0.4796
3.4019
-1.2425
0.6949
0.0344
0.0136
-0.0305
0.0277
-0.0392
-0.109
-0.0372
0.011
0.0048
0.19
-0.0075
-0.0393
0.1417
-0.0056
0.1778
-130.532
303.2247
3.7374
8
0.941
0.8184
0.2282
1.2559
0.1497
0.2134
0.2028
-0.2493
-0.1055
0.2716
-0.2032
0.0117
-0.0077
0.0804
0.0004
0.2459
-0.0918
-0.0454
0.2301
0.0485
0.0488
-119.1443
310.0356
16.79
9
4.7643
-7.1082
-2.2521
18.9509
3.1382
1.0705
0.2827
-0.7517
-0.4882
-0.2918
-0.525
-0.1155
-0.1453
0.3987
0.2422
0.2663
-0.0699
-0.1233
0.4411
0.2385
0.1623
-107.6925
306.869
23.7888
10
0.9043
0.924
-0.0226
1.1558
0.1019
0.0757
0.2129
-0.351
-0.2916
0.2426
-0.2758
-0.1938
0.0203
0.0661
0.0629
0.2604
-0.0691
-0.0723
0.2423
0.1256
0.1579
-126.9877
295.1397
20.345
11
0.5172
0.5881
-0.3107
0.756
-0.128
0.8426
0.3619
-0.2834
-0.1534
0.5166
-0.4001
-0.1952
0.13
0.0488
0.0382
0.4337
-0.2276
-0.1363
0.3453
0.0974
0.0508
-116.0062
308.9738
28.3741
12
1.6129
0.9015
-0.391
3.2518
0.7786
1.017
0.2606
-0.395
-0.0538
0.2337
-0.1571
0.2661
-0.1115
-0.0507
-0.1035
0.2787
-0.1623
0.0725
0.2407
0.0641
0.1279
-141.5856
303.9825
27.1501
13
1.5575
-0.3336
-0.4066
0.7692
-0.3441
0.3793
-0.0098
0.1594
-0.1238
-0.0393
-0.0308
0.0404
0.0241
-0.0011
0.0406
0.2428
0.0134
-0.0149
0.2335
0.0267
0.0187
-131.7176
247.5805
-8.4135
14
1.9894
1.9235
0.8644
6.1828
3.5338
2.4691
-0.0416
0.0324
0.0263
0.1501
0.1137
-0.1398
0.052
0.1557
-0.0721
0.191
0.0134
-0.0113
0.1885
0.0192
0.0568
-129.6208
258.7765
7.9272
15
1.6452
-0.1923
0.2004
0.7672
-0.2618
0.5868
0.0212
0.0028
0.0996
-0.0191
-0.0094
-0.0423
-0.0403
0.0824
-0.0118
0.1822
-0.0068
0.0056
0.1982
0.0122
0.0377
-109.9397
261.505
5.0509
16
2.1939
0.6204
1.4055
0.6453
-0.3721
2.2885
-0.1434
0.3551
0.0771
-0.1031
0.1035
-0.0362
-0.0484
0.145
0.0399
0.1868
-0.0078
0.0551
0.3015
0.0639
0.0887
-106.9987
261.505
-9.8004
17
1.0643
0.5097
0.3037
0.2991
0.1945
0.5614
-0.0478
0.2841
0.0192
-0.1067
0.0873
-0.0034
0.0261
0.165
-0.0395
0.2229
0.0095
-0.0043
0.2718
0.0259
0.0089
-120.7553
255.9682
-14.3562
18
1.2595
-1.0191
-0.6385
1.7769
0.649
0.8412
0.0538
0.2034
0.1582
-0.1052
-0.0375
0.1136
0.0327
0.0565
-0.0163
0.1944
-0.0116
-0.0313
0.1891
0.0499
0.0914
-131.9764
263.6581
-2.399
19
0.3706
0.1944
0.0955
0.3318
-0.0018
0.0437
-0.0059
0.1287
0.0398
-0.0493
0.0142
0.0916
0.0381
0.0201
-0.0083
0.215
-0.0062
-0.02
0.2172
0.0097
0.0727
-138.6669
248.9276
-8.4583
20
0.4435
0.7104
-0.174
1.7882
-0.0919
0.1592
-0.0598
0.0942
0.0208
-0.0447
-0.0065
0.134
0.0558
-0.0175
0.0664
0.1884
0.0123
-0.0266
0.2021
0.0253
0.1135
-145.1473
245.7897
-7.3128
21
0.4435
-1.3275
0.4606
5.7495
-1.9605
0.669
0.1126
0.027
0.0584
-0.3171
0.0263
0.4227
0.1133
-0.0097
-0.1389
0.1414
-0.0011
0.0003
0.1768
0.0246
0.2165
-149.4403
270.1315
6.6642
22
0.4735
0.1066
0.0932
0.9214
0.2945
0.5372
0.0054
0.0123
-0.0036
0.0582
-0.0118
0.0594
0.087
0.0223
0.0064
0.1646
-0.008
0.0044
0.1584
0.0276
0.1179
-143.4767
245.6868
6.3702
23
2.5229
0.5301
-1.0185
2.1467
-1.2505
5.2408
-0.0958
0.0034
0.2483
0.2947
-0.1151
0.1477
0.0548
-0.3506
0.2109
0.1861
-0.0101
0.0137
0.1504
-0.0361
0.1652
-147.1453
250.6218
18.402
24
0.9533
-0.9306
-0.3552
1.8915
0.6164
0.697
-0.0385
-0.1406
0.0472
0.2295
0.002
-0.0157
0.0809
0.0134
0.0365
0.2195
-0.0149
-0.0068
0.1972
0.0252
0.0509
-142.5416
250.4549
19.5543
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
28 - 55
2
X-RAY DIFFRACTION
2
A
64 - 84
3
X-RAY DIFFRACTION
3
A
85 - 129
4
X-RAY DIFFRACTION
4
A
130 - 185
5
X-RAY DIFFRACTION
5
A
186 - 217
6
X-RAY DIFFRACTION
6
A
218 - 335
7
X-RAY DIFFRACTION
7
A
336 - 375
8
X-RAY DIFFRACTION
8
A
376 - 450
9
X-RAY DIFFRACTION
9
A
451 - 464
10
X-RAY DIFFRACTION
10
A
465 - 517
11
X-RAY DIFFRACTION
11
A
518 - 546
12
X-RAY DIFFRACTION
12
A
547 - 640
13
X-RAY DIFFRACTION
13
B
28 - 63
14
X-RAY DIFFRACTION
14
B
64 - 86
15
X-RAY DIFFRACTION
15
B
87 - 185
16
X-RAY DIFFRACTION
16
B
186 - 239
17
X-RAY DIFFRACTION
17
B
240 - 335
18
X-RAY DIFFRACTION
18
B
336 - 375
19
X-RAY DIFFRACTION
19
B
376 - 425
20
X-RAY DIFFRACTION
20
B
426 - 487
21
X-RAY DIFFRACTION
21
B
488 - 504
22
X-RAY DIFFRACTION
22
B
505 - 587
23
X-RAY DIFFRACTION
23
B
588 - 602
24
X-RAY DIFFRACTION
24
B
603 - 642
+
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