BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE AUTHORS STATE THAT SIZE EXCLUSION CHROMATOGRAPHY (SEC) AND STATIC LIGHT SCATTERING SUPPORT THE ASSIGNMENT OF THE BIOLOGICAL OLIGOMERIZATION STATE AS A DIMER.
BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). SEE FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY (SEC) AND STATIC LIGHT SCATTERING SUPPORT THE ASSIGNMENT OF THE BIOLOGICAL OLIGOMERIZATION STATE AS A DIMER. GENERATING THE BIOMOLECULE COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. BIOMOLECULE: 1 APPLY THE FOLLOWING TO CHAINS: A BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 BIOMT2 2 0.000000 -1.000000 0.000000 69.1930 BIOMT3 2 0.000000 0.000000 -1.000000 453.518 BIOMOLECULE: 2 APPLY THE FOLLOWING TO CHAINS: B, C BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
-
Components
#1: Protein
Probable2-phosphosulfolactatephosphatase
Mass: 28017.225 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Gene: comB / Production host: Escherichia coli (E. coli) References: UniProt: Q97E82, 2-phosphosulfolactate phosphatase
Resolution: 2.49→50 Å / Num. obs: 22838 / % possible obs: 85.39 % / Redundancy: 4.5 % / Biso Wilson estimate: 50.62 Å2 / Rsym value: 0.048 / Net I/σ(I): 24.38
Reflection shell
Resolution: 2.49→2.53 Å / Redundancy: 1.34 % / Mean I/σ(I) obs: 3.19 / Num. unique all: 377 / Rsym value: 0.153 / % possible all: 29.22
-
Processing
Software
Name
Version
Classification
DENZO
datareduction
SCALEPACK
datascaling
SHELXD
phasing
autoSHARP
phasing
REFMAC
5.2.0005
refinement
Refinement
Method to determine structure: MAD / Resolution: 2.49→38.7 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU B: 19.135 / SU ML: 0.206 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.312 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. (3) THE NOMINAL RESOLUTION OF THE DATA IS 2.6 A, WITH 1,104 OBSERVED REFLECTIONS ...Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. (3) THE NOMINAL RESOLUTION OF THE DATA IS 2.6 A, WITH 1,104 OBSERVED REFLECTIONS BETWEEN 2.6-2.49 A (34% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22938
1159
5.1 %
RANDOM
Rwork
0.18994
-
-
-
obs
0.19201
21601
85.47 %
-
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: 38.679 Å2
Baniso -1
Baniso -2
Baniso -3
1-
3.6 Å2
0 Å2
0 Å2
2-
-
-0.27 Å2
0 Å2
3-
-
-
-3.33 Å2
Refinement step
Cycle: LAST / Resolution: 2.49→38.7 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5478
0
32
93
5603
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
5565
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
5219
X-RAY DIFFRACTION
r_angle_refined_deg
1.509
1.987
7499
X-RAY DIFFRACTION
r_angle_other_deg
0.829
3
12187
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.772
5
705
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.539
25.656
221
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.541
15
1082
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.575
15
21
X-RAY DIFFRACTION
r_chiral_restr
0.082
0.2
900
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
6059
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
1002
X-RAY DIFFRACTION
r_nbd_refined
0.211
0.2
1220
X-RAY DIFFRACTION
r_nbd_other
0.172
0.2
5259
X-RAY DIFFRACTION
r_nbtor_other
0.087
0.2
3533
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.148
0.2
173
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.134
0.2
11
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.231
0.2
45
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.26
0.2
16
X-RAY DIFFRACTION
r_mcbond_it
0.821
1.5
3755
X-RAY DIFFRACTION
r_mcbond_other
0.166
1.5
1464
X-RAY DIFFRACTION
r_mcangle_it
0.874
2
5670
X-RAY DIFFRACTION
r_scbond_it
1.741
3
2259
X-RAY DIFFRACTION
r_scangle_it
2.733
4.5
1829
X-RAY DIFFRACTION
r_nbtor_refined
0.18
0.2
2811
Refine LS restraints NCS
Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
Dom-ID
Auth asym-ID
Number
Type
Rms dev position (Å)
Weight position
1
A
1389
tightpositional
0.04
0.05
2
B
1389
tightpositional
0.04
0.05
3
C
1389
tightpositional
0.04
0.05
1
A
2108
mediumpositional
0.22
0.5
2
B
2108
mediumpositional
0.27
0.5
3
C
2108
mediumpositional
0.28
0.5
1
A
1389
tightthermal
0.09
0.5
2
B
1389
tightthermal
0.08
0.5
3
C
1389
tightthermal
0.08
0.5
1
A
2108
mediumthermal
0.5
2
2
B
2108
mediumthermal
0.39
2
3
C
2108
mediumthermal
0.41
2
LS refinement shell
Resolution: 2.488→2.552 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.317
36
6.32 %
Rwork
0.251
534
-
obs
-
-
30.32 %
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
2.0373
-0.5148
-1.058
1.3254
0.5978
3.623
0.0402
0.2507
0.0463
-0.2352
-0.058
-0.0749
0.0934
-0.1151
0.0178
-0.2521
0.0184
-0.0135
-0.2262
-0.0131
-0.1488
23.5719
31.1688
209.5029
2
0.8165
0.0469
-0.343
3.8826
2.156
5.5828
-0.0498
-0.0753
-0.0271
0.1458
0.008
0.0981
-0.0174
-0.4456
0.0418
-0.09
0.0679
0.0285
-0.1209
0.0047
-0.1009
11.6908
46.6136
169.6232
3
1.4454
0.1007
-0.6801
3.2359
0.0902
5.6138
0.1122
0.2785
0.0912
-1.2646
-0.0903
0.1109
-0.1039
-0.2555
-0.0219
0.5287
0.0332
0.0133
-0.0406
-0.0289
-0.0935
15.9372
42.7776
134.8468
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 235
2
X-RAY DIFFRACTION
2
B
1 - 235
3
X-RAY DIFFRACTION
3
C
1 - 235
+
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