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Yorodumi- PDB-1eys: CRYSTAL STRUCTURE OF PHOTOSYNTHETIC REACTION CENTER FROM A THERMO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1eys | ||||||
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Title | CRYSTAL STRUCTURE OF PHOTOSYNTHETIC REACTION CENTER FROM A THERMOPHILIC BACTERIUM, THERMOCHROMATIUM TEPIDUM | ||||||
Components | (PHOTOSYNTHETIC REACTION ...) x 4 | ||||||
Keywords | ELECTRON TRANSPORT / MEMBRANE PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information plasma membrane light-harvesting complex / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / membrane => GO:0016020 Similarity search - Function | ||||||
Biological species | Thermochromatium tepidum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Nogi, T. / Fathir, I. / Kobayashi, M. / Nozawa, T. / Miki, K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Crystal structures of photosynthetic reaction center and high-potential iron-sulfur protein from Thermochromatium tepidum: thermostability and electron transfer. Authors: Nogi, T. / Fathir, I. / Kobayashi, M. / Nozawa, T. / Miki, K. #1: Journal: FEBS Lett. / Year: 1994 Title: Preliminary X-ray Crystallographic Studies of Photosynthetic Reaction Center from a Thermophilic Sulfur Bacterium, Chromatium tepidum Authors: Katayama, N. / Kobayashi, M. / Motojima, F. / Inaka, K. / Nozawa, T. / Miki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eys.cif.gz | 256.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eys.ent.gz | 210.3 KB | Display | PDB format |
PDBx/mmJSON format | 1eys.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1eys_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 1eys_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 1eys_validation.xml.gz | 39.6 KB | Display | |
Data in CIF | 1eys_validation.cif.gz | 54.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/1eys ftp://data.pdbj.org/pub/pdb/validation_reports/ey/1eys | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-PHOTOSYNTHETIC REACTION ... , 4 types, 4 molecules CLMH
#1: Protein | Mass: 40880.738 Da / Num. of mol.: 1 / Fragment: CYTOCHROME SUBUNIT / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) |
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#2: Protein | Mass: 31417.588 Da / Num. of mol.: 1 / Fragment: L SUBUNIT / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) |
#3: Protein | Mass: 36328.285 Da / Num. of mol.: 1 / Fragment: M SUBUNIT / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) |
#4: Protein | Mass: 28286.398 Da / Num. of mol.: 1 / Fragment: H SUBUNIT / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: Q93RD8 |
-Sugars , 1 types, 6 molecules
#6: Sugar | ChemComp-BGL / |
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-Non-polymers , 9 types, 203 molecules
#5: Chemical | ChemComp-HEM / #7: Chemical | ChemComp-BCL / #8: Chemical | #9: Chemical | ChemComp-LDA / | #10: Chemical | ChemComp-FE / | #11: Chemical | ChemComp-MQ8 / | #12: Chemical | ChemComp-CRT / | #13: Chemical | ChemComp-PEF / | #14: Water | ChemComp-HOH / | |
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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: 4.02 Å3/Da / Density % sol: 69.44 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG4000, sodium chloride, phosphate, beta-octyl-glucopyranoside, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusionDetails: Kobayashi, M., (1993) Bull. Chem. Soc. Jpn., 66, 3834. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.708 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 25, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.708 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 110923 / Num. obs: 103031 / % possible obs: 92.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.362 / Num. unique all: 6548 / % possible all: 78.6 |
Reflection | *PLUS Num. obs: 110923 / Num. measured all: 508729 |
Reflection shell | *PLUS % possible obs: 78.6 % / Mean I/σ(I) obs: 2.6 |
-Processing
Software |
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Refinement | Resolution: 2.2→10 Å / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / Rfactor Rfree: 0.312 / Rfactor Rwork: 0.302 |