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 / endoplasmic reticulum-Golgi intermediate compartment membrane / MHC class II antigen presentation / 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.: 372 / 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: 2.81 Å3/Da / Density % sol: 56.2 %
Crystal grow
Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 20.0 % (w/v) PEG 3000 0.1 M sodium citrate pH 5.6
-
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
Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.5418 Å / Relative weight: 1
Reflection
Resolution: 2→27.9 Å / Num. obs: 29396 / % possible obs: 94 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 29.8
Reflection shell
Resolution: 2→2.1 Å / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 6.9 / % possible all: 61.2
-
Processing
Software
Name
Version
Classification
REFMAC
5.8.02382018/15/10
refinement
PROTEUM2
datareduction
SCALA
datascaling
REFMAC
phasing
Refinement
Resolution: 2→27.505 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.367 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.143 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.1983
1429
-
Rwork
0.1519
-
-
all
0.154
-
-
obs
-
28534
93.97 %
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parameters
Biso mean: 17.937 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.053 Å2
0 Å2
0 Å2
2-
-
0.146 Å2
0 Å2
3-
-
-
-0.093 Å2
Refinement step
Cycle: LAST / Resolution: 2→27.505 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2759
0
128
372
3259
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.013
3008
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.018
2578
X-RAY DIFFRACTION
r_angle_refined_deg
1.838
1.709
4106
X-RAY DIFFRACTION
r_angle_other_deg
1.451
1.631
6008
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.914
5
351
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.526
22.886
149
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.701
15
439
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
23.52
15
11
X-RAY DIFFRACTION
r_chiral_restr
0.086
0.2
391
X-RAY DIFFRACTION
r_gen_planes_refined
0.011
0.02
3339
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
675
X-RAY DIFFRACTION
r_nbd_refined
0.208
0.2
617
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.187
0.2
2547
X-RAY DIFFRACTION
r_nbtor_refined
0.183
0.2
1463
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.086
0.2
1374
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.209
0.2
319
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_other
0.004
0.2
2
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.234
0.2
17
X-RAY DIFFRACTION
r_nbd_other
0.216
0.2
62
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.312
0.2
28
X-RAY DIFFRACTION
r_mcbond_it
1.031
1.071
1398
X-RAY DIFFRACTION
r_mcbond_other
1.031
1.071
1397
X-RAY DIFFRACTION
r_mcangle_it
1.737
1.597
1745
X-RAY DIFFRACTION
r_mcangle_other
1.737
1.597
1746
X-RAY DIFFRACTION
r_scbond_it
1.248
1.332
1609
X-RAY DIFFRACTION
r_scbond_other
1.248
1.334
1610
X-RAY DIFFRACTION
r_scangle_it
2.069
1.963
2356
X-RAY DIFFRACTION
r_scangle_other
2.069
1.965
2357
X-RAY DIFFRACTION
r_lrange_it
5.718
14.955
3617
X-RAY DIFFRACTION
r_lrange_other
5.719
14.969
3618
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
0.228
58
0.179
1398
2209
65.9122
0.145
2.052-2.108
0.206
89
0.181
1614
2146
79.3569
0.145
2.108-2.168
0.231
98
0.166
1837
2099
92.1868
0.136
2.168-2.235
0.224
97
0.154
1870
2036
96.611
0.128
2.235-2.307
0.207
101
0.143
1782
1941
97.0119
0.121
2.307-2.388
0.215
86
0.15
1783
1923
97.1919
0.128
2.388-2.477
0.236
110
0.151
1692
1855
97.1429
0.13
2.477-2.577
0.195
96
0.144
1656
1789
97.9318
0.124
2.577-2.691
0.176
80
0.139
1585
1696
98.1722
0.122
2.691-2.821
0.206
83
0.145
1532
1652
97.7603
0.13
2.821-2.972
0.208
75
0.141
1451
1548
98.5788
0.129
2.972-3.15
0.175
68
0.149
1406
1494
98.6613
0.138
3.15-3.364
0.166
62
0.151
1319
1398
98.784
0.144
3.364-3.629
0.214
68
0.162
1222
1304
98.9264
0.159
3.629-3.969
0.168
64
0.136
1130
1205
99.0871
0.137
3.969-4.426
0.185
47
0.13
1052
1107
99.2773
0.138
4.426-5.089
0.144
49
0.126
919
970
99.7938
0.137
5.089-6.18
0.233
44
0.174
803
853
99.2966
0.182
6.18-8.527
0.26
34
0.189
640
679
99.2636
0.199
8.527-27.546
0.218
20
0.239
408
433
98.8453
0.267
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
1.2538
0.2377
0.4134
1.3245
0.1856
1.3487
-0.0381
0.0016
0.0873
-0.078
0.0004
0.0818
-0.1397
-0.1067
0.0378
0.0563
0.0205
-0.0058
0.0215
0.0144
0.0314
-6.84
-25.289
-20.185
2
0.923
0.0793
0.0138
1.0331
0.192
0.8387
-0.0134
0.0002
-0.0303
-0.0418
0.0057
-0.109
-0.0719
0.1223
0.0077
0.0296
-0.0195
0.0096
0.03
0.0135
0.0373
17.601
-30.779
-17.978
3
0.7666
-0.0855
-0.1195
1.0635
-0.0514
0.768
-0.0114
-0.0939
0.0735
0.0689
0.0054
-0.1148
-0.1698
0.169
0.006
0.0468
-0.0411
-0.0128
0.0572
0.0014
0.028
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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