- PDB-1vlg: Crystal structure of Ferritin (TM1128) from Thermotoga maritima a... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 1vlg
Title
Crystal structure of Ferritin (TM1128) from Thermotoga maritima at 2.00 A resolution
Components
ferritin
Keywords
METAL BINDING PROTEIN / TM1128 / FERRITIN / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics
Function / homology
Function and homology information
bacterial non-heme ferritin / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / cytoplasm / cytosol Similarity search - Function
Resolution: 2→87.73 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.78 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. STRANGE DENSITY NEAR RESIDUE A23. GLYCEROL AND SULFATE ION IN THE MODEL ARE DERIVED FROM CRYSTALLIZATION SOLUTION
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.218
7069
5 %
RANDOM
Rwork
0.178
-
-
-
obs
0.18
133805
99.9 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 23.15 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.69 Å2
-0.34 Å2
0 Å2
2-
-
-0.69 Å2
0 Å2
3-
-
-
1.03 Å2
Refinement step
Cycle: LAST / Resolution: 2→87.73 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
10902
0
132
651
11685
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.021
11308
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
9892
X-RAY DIFFRACTION
r_angle_refined_deg
1.288
1.949
15222
X-RAY DIFFRACTION
r_angle_other_deg
0.803
3
23094
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.814
5
1320
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.38
25.072
621
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.941
15
2079
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.852
15
53
X-RAY DIFFRACTION
r_chiral_restr
0.078
0.2
1561
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
12537
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
2348
X-RAY DIFFRACTION
r_nbd_refined
0.213
0.2
2647
X-RAY DIFFRACTION
r_nbd_other
0.167
0.2
9696
X-RAY DIFFRACTION
r_nbtor_refined
0.187
0.2
5658
X-RAY DIFFRACTION
r_nbtor_other
0.085
0.2
5926
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.156
0.2
627
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.07
0.2
1
X-RAY DIFFRACTION
r_metal_ion_refined
0.01
0.2
2
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.187
0.2
36
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.224
0.2
133
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.182
0.2
38
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_mcbond_it
2.42
3
7250
X-RAY DIFFRACTION
r_mcbond_other
0.548
3
2696
X-RAY DIFFRACTION
r_mcangle_it
3.042
5
10527
X-RAY DIFFRACTION
r_scbond_it
5.979
8
5326
X-RAY DIFFRACTION
r_scangle_it
7.741
11
4695
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2→2.05 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.269
552
-
Rwork
0.229
9755
-
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
0.7004
-0.1535
0.9531
0.698
-0.0535
2.5772
0.0397
-0.1851
0.0898
0.0923
-0.1305
-0.0517
0.4499
-0.3309
0.0908
-0.0701
-0.1314
0.0525
-0.0516
-0.0153
-0.1645
39.5728
132.1143
147.6761
2
1.6361
-0.2688
0.1785
0.7169
-0.2838
0.4155
0.0078
0.0288
0.2208
0.0446
-0.0308
-0.0699
0.002
0.0918
0.023
-0.1501
-0.0006
0.0086
-0.169
-0.0192
-0.1261
20.0787
95.125
101.6733
3
0.1973
-0.0309
0.2676
2.471
-0.3491
1.5742
0.1355
-0.1251
-0.0726
0.1628
0.0778
0.1683
-0.07
-0.0452
-0.2133
-0.1193
-0.0377
-0.0764
-0.0445
0.0545
-0.0779
48.4927
98.9172
159.1525
4
0.8153
0.812
0.0723
1.5373
0.0934
1.1485
0.0356
0.0331
-0.0768
-0.1294
0.1172
-0.0727
0.0412
0.0378
-0.1529
-0.0943
-0.0061
-0.1081
-0.1048
0.025
-0.0648
47.9167
90.3582
135.3837
5
0.6407
0.5404
0.6337
1.0639
0.2399
0.8479
0.1273
-0.0866
0.0017
0.1432
-0.1211
-0.0949
0.1219
0.0081
-0.0063
-0.1115
0.0104
-0.0077
-0.1605
-0.028
-0.1297
24.6424
73.259
113.5978
6
2.4486
-0.4502
1.0321
0.9963
0.054
0.7152
-0.1064
-0.7237
0.3362
0.1687
0.014
-0.0159
-0.0678
-0.294
0.0924
-0.1252
-0.046
0.0239
0.1802
-0.1915
-0.0526
19.9479
148.0129
147.2422
7
2.4137
-0.8984
-1.6715
1.2777
0.8963
1.7979
0.2119
-0.035
-0.108
-0.2617
-0.2245
0.228
-0.3571
0.022
0.0125
0.0333
-0.0383
-0.1259
-0.065
-0.016
-0.0822
30.8279
121.7971
181.7764
8
1.9808
0.4438
-0.4395
1.2979
-0.2205
0.6426
-0.0895
-0.3286
-0.4768
-0.005
-0.1324
-0.0188
0.004
0.1934
0.2219
-0.066
0.013
-0.0506
-0.0137
0.088
0.1252
21.051
102.1161
194.4138
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 164
2
X-RAY DIFFRACTION
2
B
1 - 164
3
X-RAY DIFFRACTION
3
C
1 - 164
4
X-RAY DIFFRACTION
4
D
1 - 164
5
X-RAY DIFFRACTION
5
E
1 - 164
6
X-RAY DIFFRACTION
6
F
1 - 164
7
X-RAY DIFFRACTION
7
G
1 - 164
8
X-RAY DIFFRACTION
8
H
1 - 164
+
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