- PDB-2olt: Crystal structure of a phou-like protein (so_3770) from shewanell... -
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Basic information
Entry
Database: PDB / ID: 2olt
Title
Crystal structure of a phou-like protein (so_3770) from shewanella oneidensis mr-1 at 2.00 A resolution
Components
Hypothetical protein
Keywords
UNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Protein of unknown function DUF47 / Putative phosphate transport regulator / Protein of unknown function DUF47 / Phosphate transport system protein phou homolog 2; domain 2 / PhoU-like domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha / TIGR00153 family protein
Function and homology information
Biological species
Shewanella oneidensis (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
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). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A HEXAMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999
SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
Resolution: 2→29.16 Å / Num. obs: 51605 / % possible obs: 99.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.058 / Χ2: 0.995 / Net I/σ(I): 13.4
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
Diffraction-ID
% possible all
2-2.05
5.5
0.623
3630
1.08
1,2
100
2.05-2.11
5.5
0.505
3652
0.972
1,2
100
2.11-2.17
5.5
0.372
3649
1.004
1,2
100
2.17-2.24
5.6
0.3
3643
0.963
1,2
100
2.24-2.32
5.5
0.235
3654
0.919
1,2
100
2.32-2.41
5.6
0.184
3652
1.019
1,2
100
2.41-2.52
5.6
0.145
3650
0.947
1,2
100
2.52-2.65
5.5
0.101
3676
1.009
1,2
100
2.65-2.82
5.5
0.083
3676
0.986
1,2
100
2.82-3.04
5.5
0.067
3674
0.921
1,2
100
3.04-3.34
5.5
0.057
3714
1.013
1,2
100
3.34-3.83
5.5
0.052
3718
1.101
1,2
100
3.83-4.82
5.4
0.043
3762
0.937
1,2
99.9
4.82-50
5.2
0.029
3855
1.06
1,2
98.4
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
SHELX
phasing
REFMAC
5.2.0005
refinement
SCALEPACK
datascaling
PDB_EXTRACT
2
dataextraction
ADSC
QUANTUM
datacollection
DENZO
datareduction
SHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 2→29.16 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.832 / SU ML: 0.126 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.163 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. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ELECTRON DENSITY SHOWS THAT RESIDUES 0-12 OF THE A SUBUNIT, RESIDUES 0-13 OF THE B SUBUNIT AND FOR RESIDUES 0-7 OF THE C SUBUNIT ARE DISORDERED. THEREFORE THESE RESIDUES WERE NOT MODELED. ELECTRON DENSITIES FOR THE FOLLOWING REGIONS ARE ALSO DISORDERED AND WERE NOT MODELED: B149-B150, C73-C74. 5. GLYCEROL MOLECULES USED AS A CRYOPROTECTANT HAVE BEEN INCORPORATED INTO THE MODEL.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.242
2634
5.1 %
RANDOM
Rwork
0.203
-
-
-
all
0.205
-
-
-
obs
0.205
51591
99.84 %
-
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: 39.759 Å2
Baniso -1
Baniso -2
Baniso -3
1-
2.45 Å2
1.22 Å2
0 Å2
2-
-
2.45 Å2
0 Å2
3-
-
-
-3.67 Å2
Refinement step
Cycle: LAST / Resolution: 2→29.16 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4898
0
27
381
5306
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.022
5012
X-RAY DIFFRACTION
r_bond_other_d
0.003
0.02
4781
X-RAY DIFFRACTION
r_angle_refined_deg
1.565
1.987
6783
X-RAY DIFFRACTION
r_angle_other_deg
1.006
3
11050
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
2.981
5
645
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.873
25.433
208
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.753
15
902
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
10.545
15
32
X-RAY DIFFRACTION
r_chiral_restr
0.109
0.2
810
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
5524
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
910
X-RAY DIFFRACTION
r_nbd_refined
0.232
0.3
1289
X-RAY DIFFRACTION
r_nbd_other
0.162
0.3
4809
X-RAY DIFFRACTION
r_nbtor_refined
0.186
0.5
2569
X-RAY DIFFRACTION
r_nbtor_other
0.093
0.5
3049
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.197
0.5
489
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.021
0.5
4
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.181
0.3
18
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.309
0.3
123
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.291
0.5
46
X-RAY DIFFRACTION
r_mcbond_it
0.956
1.5
3313
X-RAY DIFFRACTION
r_mcbond_other
0.212
1.5
1306
X-RAY DIFFRACTION
r_mcangle_it
1.353
2
5164
X-RAY DIFFRACTION
r_scbond_it
2.459
3
1897
X-RAY DIFFRACTION
r_scangle_it
3.815
4.5
1617
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
1252
TIGHTPOSITIONAL
0.07
0.05
2
B
1252
TIGHTPOSITIONAL
0.06
0.05
3
C
1252
TIGHTPOSITIONAL
0.08
0.05
1
A
1770
MEDIUMPOSITIONAL
0.42
0.5
2
B
1770
MEDIUMPOSITIONAL
0.36
0.5
3
C
1770
MEDIUMPOSITIONAL
0.33
0.5
1
A
1252
TIGHTTHERMAL
0.17
0.5
2
B
1252
TIGHTTHERMAL
0.16
0.5
3
C
1252
TIGHTTHERMAL
0.15
0.5
1
A
1770
MEDIUMTHERMAL
0.68
2
2
B
1770
MEDIUMTHERMAL
0.69
2
3
C
1770
MEDIUMTHERMAL
0.58
2
LS refinement shell
Resolution: 2→2.052 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.297
205
-
Rwork
0.252
3564
-
obs
-
3769
99.87 %
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
1.8612
0.0318
-0.1443
2.0964
0.2353
3.6908
-0.0645
0.1696
0.1052
-0.1405
-0.0574
0.0645
-0.554
-0.0301
0.122
-0.1373
-0.0308
-0.0187
-0.2908
0.018
-0.138
4.1303
17.6564
27.5364
2
0.9389
0.0667
0.2381
0.9829
0.3186
3.8182
-0.0615
0.0904
0.0229
-0.1153
-0.0043
-0.081
-0.0784
0.5765
0.0658
-0.1479
-0.021
-0.0113
-0.0954
0.0298
-0.0864
14.327
6.4501
30.4636
3
2.0483
0.2453
1.7301
1.2518
-0.0029
5.9853
-0.1475
-0.3649
0.1556
0.2059
-0.0555
0.1256
-0.3925
-0.6536
0.203
-0.2052
-0.0108
-0.0025
-0.0616
-0.027
-0.0561
31.7281
27.7671
-12.9376
4
1.6402
-0.1067
-0.1685
1.4112
0.1117
4.8934
-0.0589
-0.1561
-0.1605
0.117
0.0131
0.0692
0.6364
-0.1662
0.0458
-0.0881
-0.0446
0.0038
-0.1199
-0.0254
0.0255
40.9211
16.0886
-16.5371
5
1.5953
0.6251
0.6237
1.7584
-0.3077
5.0167
-0.0608
-0.0529
-0.2237
-0.1368
-0.0847
-0.013
0.8784
-0.6262
0.1456
-0.0475
-0.157
0.0085
0.0348
-0.0063
-0.0764
36.1267
15.7654
41.5161
6
0.4137
-0.1679
0.134
0.9376
0.4948
6.6244
-0.0584
0.1178
0.0047
-0.1476
-0.0626
0.1429
-0.4466
-1.1412
0.121
-0.0496
0.0143
-0.0253
0.2289
-0.0249
-0.0539
34.1892
30.6271
45.0452
Refinement TLS group
Refine-ID: X-RAY DIFFRACTION / Selection: ALL
ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
1
A
A
13 - 113
14 - 114
2
2
A
A
114 - 226
115 - 227
3
3
B
B
14 - 113
15 - 114
4
4
B
B
114 - 226
115 - 227
5
5
C
C
8 - 113
9 - 114
6
6
C
C
114 - 226
115 - 227
+
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