- PDB-4d02: The crystallographic structure of Flavorubredoxin from Escherichi... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4d02
Title
The crystallographic structure of Flavorubredoxin from Escherichia coli
Components
ANAEROBIC NITRIC OXIDE REDUCTASE FLAVORUBREDOXIN
Keywords
ELECTRON TRANSPORT / FDP / NITRIC OXIDE / ROO / RUBREDOXIN / FLRD
Function / homology
Function and homology information
nitric oxide reductase activity / nitric oxide catabolic process / oxidoreductase activity, acting on other nitrogenous compounds as donors / response to nitric oxide / FMN binding / electron transfer activity / iron ion binding / protein-containing complex / identical protein binding / cytoplasm Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.78 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal grow
Method: vapor diffusion, hanging drop / pH: 6.5 Details: VAPOUR DIFFUSION (HANGING DROP) AT 34C (307 K) USING 1.0UL OF PROTEIN AT14 MG/ML WITH 1 UL OF CRYSTALLIZATION SOLUTION (0.2M NA-CACODYLATE PH 6.5, 0.2 M MGACETATE, 20% PEG8000).
Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2013 Details: LIQUID NITROGEN COOLED CHANNEL-CUT SILICON MONOCHROMATOR AND A CYLINDRICAL GRAZING INCIDENCE MIRROR
Radiation
Monochromator: SI(111) MONOCHROMATOR CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.69841 Å / Relative weight: 1
Reflection
Resolution: 1.75→129.5 Å / Num. obs: 60074 / % possible obs: 95.5 % / Observed criterion σ(I): 1.64 / Redundancy: 14.2 % / Biso Wilson estimate: 23.03 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 28.4
Reflection shell
Resolution: 1.75→1.86 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 1.64 / % possible all: 75.4
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Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
XDS
datareduction
XDS
datascaling
SHELXCD
phasing
SHELXE
modelbuilding
Refinement
Method to determine structure: SAD Starting model: NONE Resolution: 1.755→129.496 Å / SU ML: 0.13 / σ(F): 1.25 / Phase error: 15.67 / Stereochemistry target values: LS_WUNIT_K1 Details: THE REFINEMENT CONVERGED TO R- -WORK AND R-FREE OF 0.1444 AND 0.1666, RESPECTIVELY, WITH A R-FREE SET OF 5401 REFLECTIONS. THE FINAL MODEL WAS THEN REFINED VERSUS THE FULL DATA SET. THE ...Details: THE REFINEMENT CONVERGED TO R- -WORK AND R-FREE OF 0.1444 AND 0.1666, RESPECTIVELY, WITH A R-FREE SET OF 5401 REFLECTIONS. THE FINAL MODEL WAS THEN REFINED VERSUS THE FULL DATA SET. THE FOLLOWING AMINOACID RESIDUES WERE MODELED WITH SIDE CHAINS IN DOUBLED CONFORMATION SER56, ARG57, LYS125, THR185, ANS217, , ARG253, VAL290, ARG339, SER357. IT WAS ONLY MODELED THE AMINOACID RESIDUES FROM 2 TO 400, BECAUSE THE RUBREDOXIN DOMAIN AT C-TERMINAL WAS NOT VISIBLE IN THE 2FO-FC MAPS. THE NATURE OF PHOSPHATE AND CHLORIDE SOLVENT MOLECULES WAS CONFIRMED BY THEIR ANOMALOUS SIGNAL.
Rfactor
Num. reflection
% reflection
Rwork
0.1407
-
-
obs
0.1407
59089
94.31 %
Rfree
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2902
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Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Biso mean: 31 Å2
Refinement step
Cycle: LAST / Resolution: 1.755→129.496 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3206
0
58
423
3687
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.015
3375
X-RAY DIFFRACTION
f_angle_d
0.924
4563
X-RAY DIFFRACTION
f_dihedral_angle_d
13.385
1229
X-RAY DIFFRACTION
f_chiral_restr
0.034
493
X-RAY DIFFRACTION
f_plane_restr
0.003
586
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.7545-1.7745
0.0135
991
0.0135
991
X-RAY DIFFRACTION
25
1.7745-1.7954
0.3966
2809
0.3966
2809
X-RAY DIFFRACTION
71
1.7954-1.8173
0.2878
3098
0.2878
3098
X-RAY DIFFRACTION
78
1.8173-1.8403
0.2835
3299
0.2835
3299
X-RAY DIFFRACTION
83
1.8403-1.8645
0.2694
3477
0.2694
3477
X-RAY DIFFRACTION
88
1.8645-1.89
0.241
3631
0.241
3631
X-RAY DIFFRACTION
92
1.89-1.917
0.2244
3749
0.2244
3749
X-RAY DIFFRACTION
95
1.917-1.9457
0.2031
3812
0.2031
3812
X-RAY DIFFRACTION
97
1.9457-1.9761
0.1988
3928
0.1988
3928
X-RAY DIFFRACTION
100
1.9761-2.0085
0.1887
3944
0.1887
3944
X-RAY DIFFRACTION
100
2.0085-2.0431
0.1851
3942
0.1851
3942
X-RAY DIFFRACTION
100
2.0431-2.0802
0.1793
3958
0.1793
3958
X-RAY DIFFRACTION
100
2.0802-2.1203
0.1725
3880
0.1725
3880
X-RAY DIFFRACTION
100
2.1203-2.1635
0.1666
3976
0.1666
3976
X-RAY DIFFRACTION
100
2.1635-2.2106
0.1561
3973
0.1561
3973
X-RAY DIFFRACTION
100
2.2106-2.262
0.1551
3936
0.1551
3936
X-RAY DIFFRACTION
100
2.262-2.3186
0.1581
3925
0.1581
3925
X-RAY DIFFRACTION
100
2.3186-2.3813
0.1582
3927
0.1582
3927
X-RAY DIFFRACTION
100
2.3813-2.4514
0.1542
3973
0.1542
3973
X-RAY DIFFRACTION
100
2.4514-2.5305
0.1492
3943
0.1492
3943
X-RAY DIFFRACTION
100
2.5305-2.6209
0.1424
3933
0.1424
3933
X-RAY DIFFRACTION
100
2.6209-2.7259
0.1477
3951
0.1477
3951
X-RAY DIFFRACTION
100
2.7259-2.85
0.1363
3924
0.1363
3924
X-RAY DIFFRACTION
100
2.85-3.0002
0.131
3952
0.131
3952
X-RAY DIFFRACTION
100
3.0002-3.1882
0.1202
3938
0.1202
3938
X-RAY DIFFRACTION
100
3.1882-3.4344
0.1094
3927
0.1094
3927
X-RAY DIFFRACTION
100
3.4344-3.78
0.0994
3980
0.0994
3980
X-RAY DIFFRACTION
100
3.78-4.327
0.0888
3943
0.0888
3943
X-RAY DIFFRACTION
100
4.327-5.4517
0.0952
3929
0.0952
3929
X-RAY DIFFRACTION
100
5.4517-129.85
0.1287
3973
0.1287
3973
X-RAY DIFFRACTION
99
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
1.1864
0.2286
0.6764
0.8
0.6372
1.5979
0.1861
0.221
-0.3058
-0.2106
-0.1047
-0.0697
0.1947
0.027
-0.0468
0.311
0.0586
-0.0598
0.2669
-0.0625
0.2921
29.4609
45.584
22.932
2
1.7397
-0.7747
-0.5071
4.6273
0.0661
0.6045
0.0914
0.0833
0.0949
0.008
-0.0475
0.0859
0.1264
0.0431
-0.0826
0.2363
0.0233
-0.0213
0.2136
-0.0318
0.2373
28.4274
59.61
38.2545
3
0.8262
0.0885
0.4476
0.6463
0.0104
2.1655
0.0743
0.3184
-0.2229
-0.3045
-0.1538
0.0473
0.1852
-0.0212
0.0095
0.3548
0.0732
-0.0575
0.3464
-0.1054
0.2791
24.1552
48.719
16.1365
4
2.5681
-0.3776
-0.3812
2.7937
1.3245
4.9792
0.1456
0.1822
0.0073
-0.3577
-0.1974
-0.2317
-0.0484
0.2956
0.0555
0.3191
0.0835
-0.0022
0.3374
-0.0229
0.2633
34.5541
54.5371
16.3871
5
1.3484
-0.3728
-0.4662
0.9681
0.137
1.2851
0.1785
0.304
-0.0096
-0.3978
-0.1842
0.0592
-0.0543
-0.0021
0.0088
0.3886
0.0961
-0.0574
0.3351
-0.0365
0.2384
23.207
58.8622
13.3603
6
1.4506
0.6431
-0.1056
1.4224
0.1731
0.6843
0.0764
0.3327
-0.0147
-0.478
-0.102
0.2159
-0.1878
-0.1519
0.0473
0.4522
0.1148
-0.0998
0.3549
-0.0468
0.2577
16.7217
62.9856
12.5239
7
0.6841
-0.0401
-0.1357
0.5179
0.0923
0.5401
0.1159
0.2072
-0.2235
-0.2571
-0.1301
0.1971
0.065
-0.0298
0.0228
0.2904
0.0492
-0.0875
0.2674
-0.0846
0.3157
16.7615
49.4431
22.8906
8
1.3696
-1.2908
-0.4253
2.6105
0.7002
0.5298
-0.0906
0.0496
-0.1344
0.0004
0.0196
0.0583
0.1077
0.0228
0.0942
0.1865
0.0124
-0.0142
0.2294
-0.0255
0.2731
21.7219
47.7244
39.2437
9
1.0981
-0.4564
0.1589
0.743
-0.1114
0.7429
0.0433
0.1346
-0.3646
-0.1443
-0.0986
0.391
0.1132
-0.1472
0.058
0.2285
0.0081
-0.0508
0.2435
-0.082
0.3588
11.0812
47.161
29.0359
10
1.3698
-0.9016
-0.6413
0.7963
1.3339
4.2793
-0.0813
0.0275
-0.4128
0.0214
-0.1133
0.3243
0.1353
-0.2119
0.1882
0.1828
-0.0101
0.0011
0.241
-0.0441
0.3747
8.779
49.7894
41.718
11
1.2292
-0.0343
0.2605
1.2188
0.1874
0.7911
-0.0155
-0.1842
-0.1838
0.0638
0.0649
0.0099
0.0247
-0.0081
-0.0431
0.1494
0.007
-0.0067
0.2082
0.0257
0.1939
19.6104
59.6547
60.4383
12
0.7104
-0.0583
-0.093
0.4834
0.0909
0.5763
0.0219
-0.0122
-0.0319
-0.0268
-0.0067
-0.0165
-0.0404
-0.0068
-0.003
0.1593
0.0158
0.0012
0.1864
-0.0009
0.1839
18.3753
66.4573
53.0617
13
2.7393
2.1073
-1.1608
4.3733
-0.5885
1.8927
-0.0203
0.0182
-0.0862
-0.0411
-0.0292
0.3831
0.0598
-0.0104
0.1126
0.1671
0.0256
-0.0183
0.2206
-0.0038
0.2372
11.7589
65.6695
44.6435
14
1.2002
0.4535
0.5651
0.784
0.8847
1.5706
0.0341
-0.185
0.0444
-0.0196
-0.0451
-0.0149
-0.0638
-0.1839
-0.0014
0.1491
0.0158
0.009
0.2116
0.0043
0.2009
11.5136
71.4641
59.3852
15
2.8783
1.9141
1.4384
2.4727
1.7746
2.4129
0.0992
-0.3888
-0.08
0.2018
-0.1226
0.0759
0.1288
-0.131
0.0055
0.2132
0.0064
0.0293
0.3014
0.0407
0.2512
11.2274
60.2798
69.0315
16
3.4147
-1.0074
-0.4288
2.4549
0.0395
2.4131
0.2268
-0.2238
0.2846
0.0229
-0.0983
0.0137
-0.0216
0.0692
-0.1031
0.2151
0.0161
0.0062
0.2469
-0.041
0.2134
23.6317
77.9662
64.1234
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
(CHAINAANDRESID2:19)
2
X-RAY DIFFRACTION
2
(CHAINAANDRESID20:31)
3
X-RAY DIFFRACTION
3
(CHAINAANDRESID32:50)
4
X-RAY DIFFRACTION
4
(CHAINAANDRESID51:69)
5
X-RAY DIFFRACTION
5
(CHAINAANDRESID70:106)
6
X-RAY DIFFRACTION
6
(CHAINAANDRESID107:131)
7
X-RAY DIFFRACTION
7
(CHAINAANDRESID132:179)
8
X-RAY DIFFRACTION
8
(CHAINAANDRESID180:198)
9
X-RAY DIFFRACTION
9
(CHAINAANDRESID199:239)
10
X-RAY DIFFRACTION
10
(CHAINAANDRESID240:251)
11
X-RAY DIFFRACTION
11
(CHAINAANDRESID252:295)
12
X-RAY DIFFRACTION
12
(CHAINAANDRESID296:325)
13
X-RAY DIFFRACTION
13
(CHAINAANDRESID326:337)
14
X-RAY DIFFRACTION
14
(CHAINAANDRESID338:375)
15
X-RAY DIFFRACTION
15
(CHAINAANDRESID376:400)
16
X-RAY DIFFRACTION
16
(CHAINAANDRESID482:482)
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