peptidase Do / cellular response to misfolded protein / protein quality control for misfolded or incompletely synthesized proteins / serine-type peptidase activity / peptidase activity / outer membrane-bounded periplasmic space / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 736 / 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: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal grow
Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 50 MM NA CACODYLATE, 100 MM NA CITRATE, 20% ISOPROPANOL, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97949 Å / Relative weight: 1
Reflection
Resolution: 2.347→50 Å / Num. obs: 90170 / % possible obs: 97.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
% possible all
2.347-2.43
5.5
0.401
97.2
2.43-2.53
6
0.31
98
2.53-2.65
6.4
0.238
97.9
2.65-2.79
6.5
0.184
98.5
2.79-2.96
6.5
0.126
98
2.96-3.19
6.5
0.087
98.3
3.19-3.51
6.5
0.071
98.5
3.51-4.02
5.5
0.077
90.3
4.02-5.06
6.8
0.051
99.7
5.06-50
7.3
0.033
99.4
-
Phasing
Phasing
Method: molecular replacement
-
Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
PHASER
phasing
PHENIX
1.5_2
refinement
PDB_EXTRACT
3.005
dataextraction
ADSC
Quantum
datacollection
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→37.14 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.31 / σ(F): 1 / Phase error: 22.35 / Stereochemistry target values: ML Details: TO OBTAIN THE BEST POSSIBLE GEOMETRY, THIS STRUCTURE WAS REFINED WITH HYDROGENS WHOSE COORDINATES WERE DETERMINED BY THE ATTACHED HEAVY ATOM. AUTHORS STATE THAT ALTHOUGH HYDROGENS CANNOT BE ...Details: TO OBTAIN THE BEST POSSIBLE GEOMETRY, THIS STRUCTURE WAS REFINED WITH HYDROGENS WHOSE COORDINATES WERE DETERMINED BY THE ATTACHED HEAVY ATOM. AUTHORS STATE THAT ALTHOUGH HYDROGENS CANNOT BE VISUALIZED AT THIS RESOLUTION, THEY ARE PRESENT AND CONTRIBUTE TO SCATTERING. THE HYDROGENS ARE KEPT IN THIS ENTRY BECAUSE INDEPENDENT ASSESSMENT OF MANY ASPECTS OF THE GEOMETRY, INCLUDING STERIC CLASHES, REQUIRE THEIR PRESENCE. MOREOVER, REMOVING HYDROGEN ATOMS AFTER REFINEMENT MAKES INDEPENDENT ASSESSMENT OF REFINEMENT STATISTICS EFFECTIVELY IRREPRODUCIBLE.
Rfactor
Num. reflection
% reflection
Rfree
0.227
4123
4.88 %
Rwork
0.185
-
-
obs
0.187
84470
91 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.68 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Biso mean: 49.8 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.941 Å2
0 Å2
-0 Å2
2-
-
0.649 Å2
0 Å2
3-
-
-
-1.589 Å2
Refinement step
Cycle: LAST / Resolution: 2.35→37.14 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
13889
0
0
736
14625
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.004
14061
X-RAY DIFFRACTION
f_angle_d
0.883
19117
X-RAY DIFFRACTION
f_dihedral_angle_d
17.601
5092
X-RAY DIFFRACTION
f_chiral_restr
0.05
2306
X-RAY DIFFRACTION
f_plane_restr
0.004
2515
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.35-2.3748
0.2687
111
0.2051
1935
X-RAY DIFFRACTION
64
2.3748-2.4038
0.2509
125
0.1966
2500
X-RAY DIFFRACTION
83
2.4038-2.4342
0.2552
126
0.204
2561
X-RAY DIFFRACTION
86
2.4342-2.4662
0.2528
128
0.2005
2568
X-RAY DIFFRACTION
84
2.4662-2.5
0.2671
153
0.1973
2617
X-RAY DIFFRACTION
88
2.5-2.5357
0.2813
142
0.1911
2641
X-RAY DIFFRACTION
88
2.5357-2.5736
0.2834
143
0.1984
2667
X-RAY DIFFRACTION
89
2.5736-2.6138
0.229
147
0.195
2715
X-RAY DIFFRACTION
91
2.6138-2.6566
0.3216
136
0.2081
2743
X-RAY DIFFRACTION
90
2.6566-2.7024
0.27
133
0.188
2754
X-RAY DIFFRACTION
92
2.7024-2.7515
0.2604
147
0.197
2758
X-RAY DIFFRACTION
90
2.7515-2.8044
0.2681
151
0.1991
2775
X-RAY DIFFRACTION
93
2.8044-2.8617
0.2091
137
0.1862
2778
X-RAY DIFFRACTION
92
2.8617-2.9239
0.2743
156
0.1825
2833
X-RAY DIFFRACTION
95
2.9239-2.9919
0.2367
159
0.1849
2803
X-RAY DIFFRACTION
93
2.9919-3.0666
0.2199
142
0.1806
2873
X-RAY DIFFRACTION
95
3.0666-3.1495
0.2198
138
0.1809
2877
X-RAY DIFFRACTION
94
3.1495-3.2421
0.2544
158
0.1939
2869
X-RAY DIFFRACTION
95
3.2421-3.3467
0.2588
153
0.1876
2866
X-RAY DIFFRACTION
95
3.3467-3.4663
0.2205
139
0.1776
2867
X-RAY DIFFRACTION
94
3.4663-3.6049
0.219
109
0.1843
2371
X-RAY DIFFRACTION
77
3.6049-3.7688
0.2838
114
0.1947
2640
X-RAY DIFFRACTION
86
3.7688-3.9673
0.1988
117
0.1777
2904
X-RAY DIFFRACTION
94
3.9673-4.2156
0.1761
144
0.1555
2957
X-RAY DIFFRACTION
97
4.2156-4.5405
0.1731
165
0.1354
3043
X-RAY DIFFRACTION
99
4.5405-4.9965
0.1715
153
0.1401
3029
X-RAY DIFFRACTION
99
4.9965-5.7172
0.1757
164
0.1602
3069
X-RAY DIFFRACTION
99
5.7172-7.1945
0.2245
166
0.1953
3133
X-RAY DIFFRACTION
99
7.1945-37.1464
0.2124
167
0.2105
3201
X-RAY DIFFRACTION
98
+
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