- PDB-2e74: Crystal Structure of the Cytochrome b6f Complex from M.laminosus -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2.0E+74
Title
Crystal Structure of the Cytochrome b6f Complex from M.laminosus
Components
(Cytochrome b6-f complex subunit ...) x 5
Apocytochrome f
Cytochrome b6-f complex iron-sulfur subunit
Cytochrome b6Cytochrome b
Keywords
PHOTOSYNTHESIS / cytochrome F / rieske iron-sulfur protein / HEME CN
Function / homology
Function and homology information
plastoquinol--plastocyanin reductase activity / cytochrome b6f complex / plastoquinol-plastocyanin reductase / electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity / cytochrome complex assembly / photosynthetic electron transport chain / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / respiratory electron transport chain ...plastoquinol--plastocyanin reductase activity / cytochrome b6f complex / plastoquinol-plastocyanin reductase / electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity / cytochrome complex assembly / photosynthetic electron transport chain / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / metal ion binding Similarity search - Function
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→39.3 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.881 / SU B: 12.475 / SU ML: 0.217 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.437 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Many of the basic and novel features of the structure of the cyanobacterial b6f complex reported now in entries 2E74 (native), 2E75 (with ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Many of the basic and novel features of the structure of the cyanobacterial b6f complex reported now in entries 2E74 (native), 2E75 (with quinone analogue inhibitor NQNO), and 2E76 (with quinone analogue inhibitor TDS) were seen in the original 3.0 A structure that was refined in space group P61 (Science, 302:1009-, 2003; pdb entry, 1VF5). This structure was thought to be a co-complex with tridecyl-stigmatellin (TDS). This inference was based on: (i) the highest resolution of 3 A was obtained in the TDS co-crystals, the native structure having a poorer resolution; (ii) electron density outside the portal on the p-side of the quinone exchange cavity resembled the TDS ring. Because of the poorer resolution of the native complex at that time, it was not possible to check for the presence of this density in the native structure. Entry 2E74 reports a 3.0 A native structure obtained in the presence of Cd2+, which shows the density previously attributed to the TDS ring. The correct p-side position of TDS, reported in 2E76, and in agreement with its location in the C. reinhardtii b6f structure (entry 1Q90) was obtained when the DOPC lipid that was added to accelerate crystallization (PNAS,100: 5160-5163) was added after TDS. 2E76 also shows a unique second binding site for TDS on the n-side of the complex, close to the position of an axial ligand of heme cn. Entry 2E75 shows that the inhibitor NQNO occupies a similar n-side binding site. This site that is common to the binding of the two quinone analogue inhibitors implies that it is also the n-side binding site of plastoquinone. 2E74,2E75, and 2E76 were refined in space group P6122.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.26843
2740
5.1 %
RANDOM
Rwork
0.22224
-
-
-
obs
0.22454
51446
99.65 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 66.528 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.19 Å2
0.66 Å2
0 Å2
2-
-
1.19 Å2
0 Å2
3-
-
-
-1.79 Å2
Refinement step
Cycle: LAST / Resolution: 3→39.3 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
7439
0
581
5
8025
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.022
8250
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.887
2.083
11269
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.356
5
950
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.221
24.124
291
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.508
15
1236
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.386
15
26
X-RAY DIFFRACTION
r_chiral_restr
0.118
0.2
1242
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
6075
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.337
0.2
4434
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.351
0.2
5635
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.204
0.2
317
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
0.183
0.2
6
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.384
0.2
85
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.163
0.2
4
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
4.328
1.5
4859
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
6.49
2
7713
X-RAY DIFFRACTION
r_scbond_it
9.887
3
4077
X-RAY DIFFRACTION
r_scangle_it
13.579
4.5
3545
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 3→3.078 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.355
191
-
Rwork
0.313
3754
-
obs
-
-
99.95 %
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
25.0672
6.57
4.2832
3.4507
0.4587
15.3798
0.667
-1.6391
0.8401
1.0345
-0.5024
0.5444
-1.2575
-1.8198
-0.1646
0.3181
0.2071
0.6956
-0.149
-0.0492
0.4215
-77.2844
73.9075
55.0783
2
2.4919
1.3389
0.6075
3.06
1.3101
8.7815
0.4794
0.2879
0.4079
0.1092
-0.6616
1.7778
0.2622
-2.1941
0.1822
-0.1149
0.3409
0.2243
0.3395
0.0702
0.8967
-82.9856
70.6614
41.1861
3
1.324
-0.2056
-1.2707
0.185
-0.2282
2.4028
0.5028
0.1143
1.1058
0.2666
-0.1553
0.5619
-0.8957
0.2537
-0.3476
0.1306
-0.0433
0.1425
-0.1057
0.1655
0.2359
-45.7597
93.8944
18.1633
4
13.6228
-3.6517
-0.2386
5.587
-2.884
1.8901
-0.1934
0.3315
-1.874
-2.3892
0.3305
-0.0836
0.4139
0.3205
-0.1371
1.0876
0.4964
-0.5646
0.6904
-1.164
1.0867
-66.8983
20.1076
-19.0155
5
2.7477
0.0516
1.0613
3.2983
0.537
2.4513
0.2987
1.096
-0.2323
-0.2268
0.097
0.3324
0.2811
-0.0115
-0.3957
-0.2748
0.1997
-0.2201
0.5753
-0.1971
0.0474
-71.1638
56.4295
-6.7137
6
19.6418
4.4789
4.493
1.3282
1.255
1.2009
-0.4809
0.8955
1.6663
-0.2265
0.1913
0.5577
-0.8335
0.3832
0.2896
0.0427
-0.0765
0.1346
0.1291
0.3221
0.2069
-40.6738
94.1794
8.1433
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
D
100 - 148
2
X-RAY DIFFRACTION
2
D
54 - 99
3
X-RAY DIFFRACTION
2
D
149 - 179
4
X-RAY DIFFRACTION
3
D
9 - 46
5
X-RAY DIFFRACTION
4
C
171 - 233
6
X-RAY DIFFRACTION
5
C
1 - 169
7
X-RAY DIFFRACTION
5
C
236 - 251
8
X-RAY DIFFRACTION
6
C
253 - 288
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