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- PDB-2e75: Crystal Structure of the Cytochrome b6f Complex with 2-nonyl-4-hy... -

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Basic information

Entry
Database: PDB / ID: 2.0E+75
TitleCrystal Structure of the Cytochrome b6f Complex with 2-nonyl-4-hydroxyquinoline N-oxide (NQNO) from M.laminosus
Components
  • (Cytochrome b6-f complex subunit ...) x 5
  • Apocytochrome f
  • Cytochrome b6-f complex iron-sulfur subunit
  • Cytochrome b6Cytochrome b
KeywordsPHOTOSYNTHESIS / 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
Single helix bin / plastocyanin oxidoreductase / Cytochrome b6-f complex subunit 6 / Cytochrome b6-f complex iron-sulfur subunit / Cytochrome b6/f complex, subunit 5 / Cytochrome b6-f complex, subunit 8 / Cytochrome b6/f complex, subunit IV / PetM of cytochrome b6/f complex subunit 7 / Cytochrome b6, PetB / Cytochrome b6/f complex, subunit 5 superfamily ...Single helix bin / plastocyanin oxidoreductase / Cytochrome b6-f complex subunit 6 / Cytochrome b6-f complex iron-sulfur subunit / Cytochrome b6/f complex, subunit 5 / Cytochrome b6-f complex, subunit 8 / Cytochrome b6/f complex, subunit IV / PetM of cytochrome b6/f complex subunit 7 / Cytochrome b6, PetB / Cytochrome b6/f complex, subunit 5 superfamily / Cytochrome b6-f complex, subunit 8 superfamily / Cytochrome B6-F complex subunit 5 / PetN / PetM family of cytochrome b6f complex subunit 7 / Cytochrome f large domain / Cytochrome f transmembrane anchor / Cytochrome f / Cytochrome f large domain / Cytochrome f large domain superfamily / Apocytochrome F, C-terminal / Apocytochrome F, N-terminal / Cytochrome f family profile. / Single helix bin / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / : / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Rieske iron-sulphur protein / Rudiment single hybrid motif / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Helix Hairpins / Up-down Bundle / Immunoglobulin-like / Beta Barrel / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
BETA-CAROTENE / : / CHLOROPHYLL A / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / Chem-OPC / 2-NONYL-4-HYDROXYQUINOLINE N-OXIDE / Chem-SQD / Cytochrome b6 / Cytochrome b6-f complex subunit 4 ...BETA-CAROTENE / : / CHLOROPHYLL A / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / Chem-OPC / 2-NONYL-4-HYDROXYQUINOLINE N-OXIDE / Chem-SQD / Cytochrome b6 / Cytochrome b6-f complex subunit 4 / Cytochrome f / Cytochrome b6-f complex iron-sulfur subunit / Cytochrome b6-f complex subunit 6 / Cytochrome b6-f complex subunit 7 / Cytochrome b6-f complex subunit 5 / Cytochrome b6-f complex subunit 8
Similarity search - Component
Biological speciesMastigocladus laminosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 Å
AuthorsCramer, W.A. / Yamashita, E. / Zhang, H.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure of the Cytochrome b(6)f Complex: Quinone Analogue Inhibitors as Ligands of Heme c(n)
Authors: Yamashita, E. / Zhang, H. / Cramer, W.A.
History
DepositionJan 5, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome b6
B: Cytochrome b6-f complex subunit 4
C: Apocytochrome f
D: Cytochrome b6-f complex iron-sulfur subunit
E: Cytochrome b6-f complex subunit 6
F: Cytochrome b6-f complex subunit 7
G: Cytochrome b6-f complex subunit 5
H: Cytochrome b6-f complex subunit 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,62025
Polymers107,6518
Non-polymers8,96817
Water905
1
A: Cytochrome b6
B: Cytochrome b6-f complex subunit 4
C: Apocytochrome f
D: Cytochrome b6-f complex iron-sulfur subunit
E: Cytochrome b6-f complex subunit 6
F: Cytochrome b6-f complex subunit 7
G: Cytochrome b6-f complex subunit 5
H: Cytochrome b6-f complex subunit 8
hetero molecules

A: Cytochrome b6
B: Cytochrome b6-f complex subunit 4
C: Apocytochrome f
D: Cytochrome b6-f complex iron-sulfur subunit
E: Cytochrome b6-f complex subunit 6
F: Cytochrome b6-f complex subunit 7
G: Cytochrome b6-f complex subunit 5
H: Cytochrome b6-f complex subunit 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,23950
Polymers215,30316
Non-polymers17,93634
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area86420 Å2
ΔGint-960 kcal/mol
Surface area80230 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)159.164, 159.164, 362.269
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operation: X, X-Y+1, 1/6-Z.

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Components

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Protein , 3 types, 3 molecules ACD

#1: Protein Cytochrome b6 / Cytochrome b


Mass: 24245.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83791
#3: Protein Apocytochrome f


Mass: 31655.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83793
#4: Protein Cytochrome b6-f complex iron-sulfur subunit / Rieske iron-sulfur protein / Plastohydroquinone:plastocyanin oxidoreductase iron-sulfur protein / ISP / RISP


Mass: 19422.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83794, EC: 1.10.99.1

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Cytochrome b6-f complex subunit ... , 5 types, 5 molecules BEFGH

#2: Protein Cytochrome b6-f complex subunit 4 / 17 kDa polypeptide


Mass: 17687.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83792
#5: Protein/peptide Cytochrome b6-f complex subunit 6 / Cytochrome b6-f complex subunit VI / Cytochrome b6-f complex subunit petL


Mass: 3504.444 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83795
#6: Protein/peptide Cytochrome b6-f complex subunit 7 / Cytochrome b6-f complex subunit VII / Cytochrome b6-f complex subunit petM


Mass: 3843.595 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83796
#7: Protein/peptide Cytochrome b6-f complex subunit 5 / Cytochrome b6-f complex subunit V / Cytochrome b6-f complex subunit petG


Mass: 4016.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83797
#8: Protein/peptide Cytochrome b6-f complex subunit 8 / Cytochrome b6-f complex subunit VIII / Cytochrome b6-f complex subunit petN


Mass: 3276.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83798

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Non-polymers , 10 types, 22 molecules

#9: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#10: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#11: Chemical ChemComp-OPC / (7R,17E)-4-HYDROXY-N,N,N,7-TETRAMETHYL-7-[(8E)-OCTADEC-8-ENOYLOXY]-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-17-EN-1-AMINIUM 4-OXIDE / DIOLEOYL-PHOSPHATIDYLCHOLINE / Phosphatidylcholine


Mass: 801.148 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C45H87NO8P / Comment: phospholipid*YM
#12: Chemical
ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE


Mass: 496.589 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H44O11 / Comment: detergent*YM
#13: Chemical ChemComp-QNO / 2-NONYL-4-HYDROXYQUINOLINE N-OXIDE


Mass: 287.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H25NO2
#14: Chemical ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#15: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#16: Chemical ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H78O12S
#17: Chemical ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56
#18: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 6.148864 Å3/Da / Density % sol: 79.996307 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.55→137.36 Å / Num. obs: 33633 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 9 % / Biso Wilson estimate: 65.5 Å2 / Rmerge(I) obs: 0.086

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.55→49.94 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.841 / SU B: 18.1 / SU ML: 0.271 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.485 / 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.26705 1702 5.1 %RANDOM
Rwork0.20067 ---
obs0.20396 31869 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.705 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20.54 Å20 Å2
2--1.08 Å20 Å2
3----1.62 Å2
Refinement stepCycle: LAST / Resolution: 3.55→49.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7439 0 602 5 8046
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0380.0228272
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg4.0762.08511297
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.8755950
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.08924.124291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg27.969151236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.5911526
X-RAY DIFFRACTIONr_chiral_restr0.2540.21242
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026088
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.40.25229
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3940.25378
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2670.2478
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.170.28
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3490.275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.280.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.4821.54959
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it10.55927713
X-RAY DIFFRACTIONr_scbond_it16.82634175
X-RAY DIFFRACTIONr_scangle_it21.9424.53578
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.55→3.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 105 -
Rwork0.179 2326 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
112.65835.39895.05137.28293.65469.24550.8244-1.44290.79751.1262-0.48270.9272-0.7387-1.231-0.34170.23850.16660.4714-0.1012-0.05020.1512-77.896573.560355.4569
20.91090.3532-1.30617.92524.10034.5979-0.02830.24730.5609-0.2197-0.10251.3996-0.2749-0.92350.1307-0.22760.16280.08530.11330.10110.3862-83.853770.534841.6404
35.69734.3319-2.34333.5458-2.43972.68130.6327-0.07460.83040.7352-0.36840.8157-0.54390.1627-0.26440.1086-0.02340.1092-0.07290.11540.0502-46.571494.155618.4396
44.57571.5303-1.7231.4729-3.41369.025-0.4875-0.3672-0.8631-1.32130.3578-0.59681.3089-0.33660.12970.55110.3692-0.4607-0.0424-0.70160.4577-68.138520.4473-19.0529
52.98670.23851.2542.48950.87671.5480.16740.7447-0.1453-0.08330.08250.19140.0810.0088-0.2499-0.13340.0906-0.0740.2707-0.1185-0.0896-72.223256.8286-6.5313
63.46763.19970.21623.00180.13451.95730.05011.00140.30910.23280.25290.1849-0.47720.04-0.3030.04140.06120.0754-0.07580.15620.0777-41.615494.57378.4256
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D100 - 148
2X-RAY DIFFRACTION2D54 - 99
3X-RAY DIFFRACTION2D149 - 179
4X-RAY DIFFRACTION3D9 - 46
5X-RAY DIFFRACTION4C171 - 233
6X-RAY DIFFRACTION5C1 - 169
7X-RAY DIFFRACTION5C236 - 251
8X-RAY DIFFRACTION6C253 - 288

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