regulation of natural killer cell apoptotic process / Regulation of MITF-M-dependent genes involved in apoptosis / lens development in camera-type eye / cysteine-type endopeptidase inhibitor activity / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of protein ubiquitination / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity ...regulation of natural killer cell apoptotic process / Regulation of MITF-M-dependent genes involved in apoptosis / lens development in camera-type eye / cysteine-type endopeptidase inhibitor activity / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of protein ubiquitination / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / regulation of cell population proliferation / regulation of apoptotic process / regulation of cell cycle / protein ubiquitination / centrosome / negative regulation of apoptotic process / apoptotic process / Golgi apparatus / enzyme binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function
Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / : / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site ...Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / : / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology
Resolution: 2.3→2.38 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1277 / % possible all: 100
-
Processing
Software
Name
Version
Classification
REFMAC
5.2.0005
refinement
MAR345
345
datacollection
DENZO
datareduction
SCALEPACK
datascaling
Refinement
Method to determine structure: FOURIER SYNTHESIS Starting model: 1.3 A structure of the ML-IAP/XIAP protein bound to a different peptidomimetic, with the ligand and surrounding waters removed Resolution: 2.3→24.34 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.803 / SU ML: 0.126 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22385
644
4.9 %
RANDOM
Rwork
0.18783
-
-
-
all
0.189
13116
-
-
obs
0.18954
12395
99.71 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 1.897 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.8 Å2
0 Å2
0 Å2
2-
-
-0.8 Å2
0 Å2
3-
-
-
1.6 Å2
Refinement step
Cycle: LAST / Resolution: 2.3→24.34 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1494
0
95
135
1724
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.021
1660
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1401
X-RAY DIFFRACTION
r_angle_refined_deg
1.363
1.987
2247
X-RAY DIFFRACTION
r_angle_other_deg
0.827
3
3256
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.036
5
183
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.892
23.038
79
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.717
15
223
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.587
15
8
X-RAY DIFFRACTION
r_chiral_restr
0.077
0.2
209
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
1835
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
379
X-RAY DIFFRACTION
r_nbd_refined
0.218
0.2
344
X-RAY DIFFRACTION
r_nbd_other
0.182
0.2
1363
X-RAY DIFFRACTION
r_nbtor_refined
0.191
0.2
787
X-RAY DIFFRACTION
r_nbtor_other
0.083
0.2
803
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.187
0.2
97
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.125
0.2
13
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.206
0.2
62
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.154
0.2
13
X-RAY DIFFRACTION
r_mcbond_it
0.463
2.5
1181
X-RAY DIFFRACTION
r_mcbond_other
0.051
2.5
380
X-RAY DIFFRACTION
r_mcangle_it
0.611
5
1464
X-RAY DIFFRACTION
r_scbond_it
0.528
2.5
904
X-RAY DIFFRACTION
r_scangle_it
0.849
5
783
LS refinement shell
Resolution: 2.3→2.359 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.218
52
-
Rwork
0.223
883
-
obs
-
-
100 %
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
3.3511
-1.6301
-0.4687
3.9084
-0.093
2.5476
0.0747
0.2339
-0.0061
-0.3263
-0.1114
-0.0276
0.0363
0.0052
0.0367
-0.1562
0.0079
0.0077
-0.1617
0.0018
-0.181
84.8665
68.1706
22.224
2
1.6325
-0.8708
0.4913
4.302
-1.7073
2.6394
0.0534
-0.2011
-0.056
0.2194
0.0243
0.075
-0.0804
-0.0373
-0.0777
-0.1523
-0.0308
0.0138
-0.1874
-0.0042
-0.1883
77.9314
59.747
50.1759
3
3.0056
0.5542
9.2728
0.1022
1.7098
28.6078
0.2548
0.9836
-0.6483
-1.1625
-0.1655
0.5867
-0.1137
-1.0681
-0.0893
0.0453
0.0661
-0.1426
-0.0319
-0.0352
-0.0188
79.2975
62.4305
14.3987
4
2.9555
5.4224
-0.0163
16.5146
-8.704
11.4592
-0.4995
-0.2447
0.1125
0.4578
-0.3351
1.4919
2.1493
-0.3262
0.8346
-0.181
-0.0639
0.058
0.0099
-0.0021
0.0816
68.0404
55.1367
48.5896
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
X-RAY DIFFRACTION
1
A
A
78 - 167
39 - 128
2
X-RAY DIFFRACTION
1
A
C
1001
1
3
X-RAY DIFFRACTION
2
B
B
78 - 171
39 - 132
4
X-RAY DIFFRACTION
2
B
D
1001
1
5
X-RAY DIFFRACTION
3
A
F
501
1
6
X-RAY DIFFRACTION
4
B
G
501
1
+
About Yorodumi
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi