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Yorodumi- PDB-4h13: Crystal Structure of the Cytochrome b6f Complex from Mastigocladu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4h13 | |||||||||
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Title | Crystal Structure of the Cytochrome b6f Complex from Mastigocladus laminosus with TDS | |||||||||
Components |
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Keywords | PHOTOSYNTHESIS / Alpha helix / beta sheet / Plastoquinol-plastocyanin oxidoreductase / Plastocyanin / Thylakoid membrane | |||||||||
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 | |||||||||
Biological species | Mastigocladus laminosus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 Å | |||||||||
Authors | Hasan, S.S. / Yamashita, E. / Baniulis, D. / Cramer, W.A. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Quinone-dependent proton transfer pathways in the photosynthetic cytochrome b6f complex Authors: Hasan, S.S. / Yamashita, E. / Baniulis, D. / Cramer, W.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4h13.cif.gz | 414.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h13.ent.gz | 339.4 KB | Display | PDB format |
PDBx/mmJSON format | 4h13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/4h13 ftp://data.pdbj.org/pub/pdb/validation_reports/h1/4h13 | HTTPS FTP |
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-Related structure data
Related structure data | 4h0lC 4h44C 2e76S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 3 types, 3 molecules ACD
#1: Protein | Mass: 24245.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83791 |
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#3: Protein | 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 | Mass: 19422.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83794, EC: 1.10.9.1 |
-Cytochrome b6-f complex subunit ... , 5 types, 5 molecules BEFGH
#2: Protein | Mass: 17687.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83792 |
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#5: Protein/peptide | 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 | 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 | 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 | Mass: 3276.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83798 |
-Non-polymers , 14 types, 43 molecules
#9: Chemical | ChemComp-CD / | ||||||||||||||||||||||||
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#10: Chemical | ChemComp-HEM / #11: Chemical | #12: Chemical | ChemComp-MYS / | #13: Chemical | ChemComp-8K6 / | #14: Chemical | #15: Chemical | #16: Chemical | ChemComp-CLA / | #17: Chemical | ChemComp-7PH / ( | #18: Chemical | ChemComp-SQD / | #19: Chemical | ChemComp-FES / | #20: Chemical | ChemComp-OCT / | #21: Chemical | ChemComp-BCR / | #22: Water | ChemComp-HOH / | |
-Details
Sequence details | THIS RESIDUE WAS PRO ACCORDING TO THE PREVIOUS VERSION OF DATABASE P83793 (CYF_MASLA). |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.02 Å3/Da / Density % sol: 79.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3.07→34.57 Å / Num. all: 50067 / Num. obs: 50067 / Biso Wilson estimate: 91.83 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 2E76 Resolution: 3.07→34.567 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.912 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8118 / SU ML: 0.37 / σ(F): 1.35 / Phase error: 25.08 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 max: 316.07 Å2 / Biso mean: 115.8209 Å2 / Biso min: 0 Å2
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Refinement step | Cycle: LAST / Resolution: 3.07→34.567 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18
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