dipeptidyl-peptidase I / peptidase activator activity involved in apoptotic process / positive regulation of proteolysis involved in protein catabolic process / negative regulation of myelination / positive regulation of microglial cell activation / Cargo concentration in the ER / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding / COPII-coated ER to Golgi transport vesicle ...dipeptidyl-peptidase I / peptidase activator activity involved in apoptotic process / positive regulation of proteolysis involved in protein catabolic process / negative regulation of myelination / positive regulation of microglial cell activation / Cargo concentration in the ER / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding / COPII-coated ER to Golgi transport vesicle / phosphatase binding / cysteine-type peptidase activity / MHC class II antigen presentation / endoplasmic reticulum-Golgi intermediate compartment membrane / : / proteolysis involved in protein catabolic process / positive regulation of apoptotic signaling pathway / T cell mediated cytotoxicity / : / azurophil granule lumen / protein-folding chaperone binding / collagen-containing extracellular matrix / lysosome / immune response / endoplasmic reticulum lumen / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / serine-type endopeptidase activity / centrosome / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane Similarity search - Function
Cathepsin C, exclusion domain / Cysteine proteinases. Chain C / Cathepsin C exclusion / Cathepsin C, exclusion domain superfamily / Cathepsin C / Cathepsin C exclusion domain / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site ...Cathepsin C, exclusion domain / Cysteine proteinases. Chain C / Cathepsin C exclusion / Cathepsin C, exclusion domain superfamily / Cathepsin C / Cathepsin C exclusion domain / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Lipocalin / Papain-like cysteine peptidase superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta Similarity search - Domain/homology
Dipeptidylpeptidase1 / Cathepsin C / Cathepsin J / Dipeptidyl peptidase I / DPPI / Dipeptidyl transferase
Mass: 13500.163 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTSC, CPPI / Cell line (production host): BTI-TN-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53634, dipeptidyl-peptidase I
#2: Protein
Dipeptidylpeptidase1 / Cathepsin C / Cathepsin J / Dipeptidyl peptidase I / DPPI / Dipeptidyl transferase
Mass: 18302.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTSC, CPPI / Cell line (production host): BTI-TN-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53634, dipeptidyl-peptidase I
#3: Protein
Dipeptidylpeptidase1 / Cathepsin C / Cathepsin J / Dipeptidyl peptidase I / DPPI / Dipeptidyl transferase
Mass: 7583.444 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTSC, CPPI / Cell line (production host): BTI-TN-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53634, dipeptidyl-peptidase I
Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.79 Å3/Da / Density % sol: 55.94 %
Crystal grow
Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 20.0 % (w/v) PEG 3000 0.2 M ammonium citrate dibasic 2.5 mM DTT
-
Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source
Source: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.5418 Å
Detector
Type: Bruker Platinum 135 / Detector: CCD / Date: Dec 1, 2010
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.5418 Å / Relative weight: 1
Reflection
Resolution: 2→28.3 Å / Num. obs: 30537 / % possible obs: 98.2 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 23.8
Reflection shell
Resolution: 2→2.1 Å / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 6.1 / % possible all: 85.5
-
Processing
Software
Name
Version
Classification
REFMAC
5.8.02382018/15/10
refinement
PROTEUM
datareduction
PROTEUM
datascaling
REFMAC
phasing
Refinement
Method to determine structure: FOURIER SYNTHESIS / Resolution: 2→28.231 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.767 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.144 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.2034
1466
-
Rwork
0.1596
-
-
all
0.162
-
-
obs
-
29338
97.252 %
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parameters
Biso mean: 20.023 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.146 Å2
0 Å2
0 Å2
2-
-
0.417 Å2
0 Å2
3-
-
-
-0.563 Å2
Refinement step
Cycle: LAST / Resolution: 2→28.231 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2759
0
127
349
3235
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.013
3061
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.018
2619
X-RAY DIFFRACTION
r_angle_refined_deg
1.931
1.709
4195
X-RAY DIFFRACTION
r_angle_other_deg
1.462
1.633
6113
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
19.05
5.346
376
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
29.536
22.933
150
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.674
15
436
X-RAY DIFFRACTION
r_dihedral_angle_other_3_deg
4.877
15
3
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
23.757
15
11
X-RAY DIFFRACTION
r_chiral_restr
0.091
0.2
403
X-RAY DIFFRACTION
r_gen_planes_refined
0.012
0.02
3705
X-RAY DIFFRACTION
r_gen_planes_other
0.004
0.02
691
X-RAY DIFFRACTION
r_nbd_refined
0.229
0.2
634
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.19
0.2
2602
X-RAY DIFFRACTION
r_nbtor_refined
0.184
0.2
1489
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.093
0.2
1337
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.212
0.2
297
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_other
0.093
0.2
1
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.244
0.2
19
X-RAY DIFFRACTION
r_nbd_other
0.216
0.2
67
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.33
0.2
22
X-RAY DIFFRACTION
r_mcbond_it
1.396
1.401
1424
X-RAY DIFFRACTION
r_mcbond_other
1.395
1.4
1423
X-RAY DIFFRACTION
r_mcangle_it
2.349
2.092
1786
X-RAY DIFFRACTION
r_mcangle_other
2.349
2.093
1787
X-RAY DIFFRACTION
r_scbond_it
1.358
1.574
1637
X-RAY DIFFRACTION
r_scbond_other
1.358
1.575
1638
X-RAY DIFFRACTION
r_scangle_it
2.225
2.318
2401
X-RAY DIFFRACTION
r_scangle_other
2.225
2.319
2402
X-RAY DIFFRACTION
r_lrange_it
5.599
18.088
3671
X-RAY DIFFRACTION
r_lrange_other
5.601
18.085
3671
LS refinement shell
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Num. reflection all
% reflection obs (%)
WRfactor Rwork
2-2.052
0.202
75
0.185
1741
2165
83.8799
0.161
2.052-2.108
0.255
100
0.189
1862
2154
91.0863
0.165
2.108-2.168
0.246
104
0.175
1914
2085
96.7866
0.153
2.168-2.235
0.213
93
0.171
1906
2024
98.7648
0.148
2.235-2.307
0.218
103
0.159
1809
1934
98.8625
0.14
2.307-2.388
0.231
88
0.163
1782
1894
98.7328
0.144
2.388-2.477
0.229
105
0.164
1728
1849
99.1347
0.146
2.477-2.578
0.209
101
0.144
1671
1787
99.1606
0.132
2.578-2.691
0.16
79
0.149
1581
1672
99.2823
0.138
2.691-2.821
0.239
88
0.163
1564
1665
99.2192
0.156
2.821-2.972
0.209
72
0.155
1428
1512
99.2063
0.152
2.972-3.15
0.167
67
0.155
1408
1492
98.8606
0.155
3.15-3.365
0.22
65
0.165
1313
1388
99.2795
0.17
3.365-3.63
0.22
65
0.165
1227
1302
99.2319
0.175
3.63-3.97
0.161
67
0.139
1128
1209
98.842
0.153
3.97-4.428
0.167
49
0.131
1038
1094
99.3601
0.153
4.428-5.092
0.136
45
0.123
909
956
99.7908
0.151
5.092-6.186
0.22
44
0.176
804
849
99.8822
0.199
6.186-8.546
0.246
35
0.191
640
676
99.8521
0.226
8.546-28.231
0.266
21
0.239
408
431
99.536
0.305
Refinement TLS params.
Details: U values: with tls added / 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
1.6197
-0.0383
0.4764
1.2551
0.1648
1.2324
-0.0107
0.0025
0.0879
-0.0938
-0.0211
0.1128
-0.1275
-0.1008
0.0318
0.0337
0.0198
0.0013
0.0214
0.0175
0.0446
-6.84
-25.289
-20.185
2
1.1303
0.0273
-0.0689
1.2679
0.2074
0.8449
-0.0148
-0.0109
-0.0433
-0.0044
0.0004
-0.1286
-0.0478
0.1379
0.0145
0.0049
-0.0086
0.0006
0.0298
0.0161
0.0357
17.601
-30.779
-17.978
3
0.9605
0.0522
-0.1637
1.2573
0.3884
1.1713
0.019
-0.1569
0.0732
0.1278
0.0034
-0.1607
-0.1228
0.2362
-0.0223
0.0792
-0.0386
-0.0191
0.1131
0.0114
0.0707
20.239
-24.406
-8.854
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
ALL
A
1 - 118
2
X-RAY DIFFRACTION
2
ALL
B
206 - 367
3
X-RAY DIFFRACTION
3
ALL
C
372 - 439
+
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