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- PDB-1q90: Structure of the cytochrome b6f (plastohydroquinone : plastocyani... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1q90 | |||||||||
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Title | Structure of the cytochrome b6f (plastohydroquinone : plastocyanin oxidoreductase) from Chlamydomonas reinhardtii | |||||||||
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![]() | PHOTOSYNTHESIS / MEMBRANE PROTEIN COMPLEX / ELECTRON TRANSFER / OXYDOREDUCTASE / CHLOROPHYLL / BETA-CAROTENE / STIGMATELLIN / SULFOQUINOVOSYLDIACYLGLYCEROL / MONOGALACTOSYLDIACYLGLYCEROL | |||||||||
Function / homology | ![]() nonphotochemical quenching / cytochrome b6f complex / plastoquinol-plastocyanin reductase / electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity / response to karrikin / cytochrome complex assembly / : / chloroplast envelope / photosynthetic electron transport chain / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity ...nonphotochemical quenching / cytochrome b6f complex / plastoquinol-plastocyanin reductase / electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity / response to karrikin / cytochrome complex assembly / : / chloroplast envelope / photosynthetic electron transport chain / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / chloroplast thylakoid membrane / : / photosynthesis / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / membrane => GO:0016020 / electron transfer activity / defense response to bacterium / iron ion binding / heme binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Stroebel, D. / Choquet, Y. / Popot, J.-L. / Picot, D. | |||||||||
![]() | ![]() Title: An Atypical Haem in the Cytochrome B6F Complex Authors: Stroebel, D. / Choquet, Y. / Popot, J.-L. / Picot, D. #1: ![]() Title: Chimeric Fusions of Subunits IV and PET L in the Cytochrome B6F complex of chlamydomonas reinhardtii: structural implications and consequences on state transitions Authors: Zito, F. / Vinh, J. / Popot, J.L. / Finazzi, G. | |||||||||
History |
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Remark 999 | SEQUENCE Apocytochrome f (chain A): 6His tag at C-terminus, residues 287-292 Rieske Proteins ...SEQUENCE Apocytochrome f (chain A): 6His tag at C-terminus, residues 287-292 Rieske Proteins (chains C,R): sequence numbering includes signal peptide (residues 1-30). Please see Remark 3 - Other Refinement Remarks Subunit 7 (chain M): sequence numbering includes signal peptide (residues 1-60). PETN subunit (chain N): sequence numbering includes the signal peptide but the beginning of the mature sequence is unknown. Sequence used is that of volvox carteri f. nagariensis according to reference 1. | |||||||||
Remark 600 | HETEROGEN Ligand SQD: acyl chains unidentified Ligand LFA: putative alkyl chain of lipid Ligand LMG: ...HETEROGEN Ligand SQD: acyl chains unidentified Ligand LFA: putative alkyl chain of lipid Ligand LMG: putative, alkyl chains unidentified |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 203.4 KB | Display | ![]() |
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PDB format | ![]() | 170 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | The second part of the biological assembly is generated by the two fold axis: -x+1,-y+2,z |
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Components
-Protein , 3 types, 3 molecules ABD
#1: Protein | Mass: 32109.834 Da / Num. of mol.: 1 / Fragment: Residues 1-292 / Mutation: 6 His tag at C-terminus Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 24184.531 Da / Num. of mol.: 1 / Fragment: Residues 4-215 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Protein | Mass: 17305.580 Da / Num. of mol.: 1 / Fragment: Residues 4-159 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Cytochrome B6-F complex iron-sulfur ... , 2 types, 2 molecules CR
#3: Protein | Mass: 13660.400 Da / Num. of mol.: 1 / Fragment: Soluble domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#5: Protein/peptide | Mass: 4707.349 Da / Num. of mol.: 1 / Fragment: Transmembrane domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P23230, UniProt: P49728*PLUS, EC: 1.10.99.1 |
-Cytochrome b6f complex subunit ... , 4 types, 4 molecules GLMN
#6: Protein/peptide | Mass: 3984.786 Da / Num. of mol.: 1 / Fragment: Residues 1-30 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#7: Protein/peptide | Mass: 3438.341 Da / Num. of mol.: 1 / Fragment: Residues 1-32 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#8: Protein/peptide | Mass: 4037.782 Da / Num. of mol.: 1 / Fragment: Residues 62-95 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#9: Protein/peptide | Mass: 3283.840 Da / Num. of mol.: 1 / Fragment: Residues 68-98 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 9 types, 14 molecules ![](data/chem/img/HEC.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/LFA.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/TDS.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/LFA.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/TDS.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/HOH.gif)
#10: Chemical | ChemComp-HEC / #11: Chemical | ChemComp-BCR / | #12: Chemical | ChemComp-LFA / | #13: Chemical | ChemComp-FES / | #14: Chemical | ChemComp-CLA / | #15: Chemical | ChemComp-TDS / | #16: Chemical | #17: Chemical | ChemComp-SQD / | #18: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 7.06 Å3/Da / Density % sol: 82 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: Reservoir: 25% PEG-MME 350, 40 millimolar TRIS HCL PH 8, 40 millimolar nacl, 0.2 millimolar laurylmaltoside, 30% glycerol. Drop: 1.3 microliter protein + 0.7 microliter reservoir, VAPOR ...Details: Reservoir: 25% PEG-MME 350, 40 millimolar TRIS HCL PH 8, 40 millimolar nacl, 0.2 millimolar laurylmaltoside, 30% glycerol. Drop: 1.3 microliter protein + 0.7 microliter reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 15, 2002 |
Radiation | Monochromator: Two Si crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00799 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→35 Å / Num. obs: 56687 / % possible obs: 99.6 % / Observed criterion σ(I): 1.8 / Redundancy: 4.6 % / Rsym value: 0.089 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 3.1→3.27 Å / Rsym value: 0.39 / % possible all: 99.6 |
Reflection | *PLUS Redundancy: 4.3 % / Rmerge(I) obs: 0.089 |
Reflection shell | *PLUS % possible obs: 99.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.8 |
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Processing
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Refinement | Method to determine structure: ![]() Details: In a B6F dimer, a rieske protein is anchored in one monomer by its transmembrane domain (residues 33-71), even though its soluble domain (residues 80-183 and 185-206) lies on the other ...Details: In a B6F dimer, a rieske protein is anchored in one monomer by its transmembrane domain (residues 33-71), even though its soluble domain (residues 80-183 and 185-206) lies on the other monomer. This is why the rieske chain of one monomer is divided into two parts corresponding to two different rieske proteins. The linker (residues 72-79) is not visible. In the soluble domain, the sub-domain corresponding to residues 80-130 and 177-206 is not well defined.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 64.6136 Å2 / ksol: 0.354968 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.9 Å2
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Refine analyze | Luzzati coordinate error free: 0.43 Å / Luzzati sigma a free: 0.53 Å | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→34.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3.1 Å / Lowest resolution: 35 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 3.21 Å / Rfactor Rfree: 0.36 / Rfactor Rwork: 0.34 |