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Yorodumi- PDB-1l9j: X-Ray Structure of the Cytochrome-c(2)-Photosynthetic Reaction Ce... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l9j | ||||||
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Title | X-Ray Structure of the Cytochrome-c(2)-Photosynthetic Reaction Center Electron Transfer Complex from Rhodobacter sphaeroides in Type I Co-Crystals | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / bacterial photosynthesis / electron transfer proteins / protein-protein interactions / membrane proteins / protein complexes | ||||||
Function / homology | Function and homology information : / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / photosynthesis / membrane => GO:0016020 / periplasmic space ...: / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / photosynthesis / membrane => GO:0016020 / periplasmic space / electron transfer activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodobacter sphaeroides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | ||||||
Authors | Axelrod, H.L. / Abresch, E.C. / Okamura, M.Y. / Yeh, A.P. / Rees, D.C. / Feher, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: X-ray structure determination of the cytochrome c2: reaction center electron transfer complex from Rhodobacter sphaeroides. Authors: Axelrod, H.L. / Abresch, E.C. / Okamura, M.Y. / Yeh, A.P. / Rees, D.C. / Feher, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l9j.cif.gz | 402.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l9j.ent.gz | 323.3 KB | Display | PDB format |
PDBx/mmJSON format | 1l9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/1l9j ftp://data.pdbj.org/pub/pdb/validation_reports/l9/1l9j | HTTPS FTP |
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-Related structure data
Related structure data | 1l9bC 1aijS 1cxcS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-REACTION CENTER PROTEIN ... , 3 types, 6 molecules LRMSHT
#1: Protein | Mass: 31346.389 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R26 / References: UniProt: P02954, UniProt: P0C0Y8*PLUS #2: Protein | Mass: 34398.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R26 / References: UniProt: P02953, UniProt: P0C0Y9*PLUS #3: Protein | Mass: 28066.322 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R26 / References: UniProt: P11846, UniProt: P0C0Y7*PLUS |
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-Protein , 1 types, 2 molecules CD
#4: Protein | Mass: 13488.064 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R26 / References: UniProt: P00095, UniProt: P0C0X8*PLUS |
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-Non-polymers , 8 types, 153 molecules
#5: Chemical | ChemComp-BCL / #6: Chemical | ChemComp-BPH / #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-LDA / #11: Chemical | #12: 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: 3.59 Å3/Da / Density % sol: 65.74 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG 4000, lauryl-dimethylamine-N-oxide, heptane-1,2,3-triol, tricine buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 19 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 10, 2000 / Details: Flat mirror (vertical focusing) |
Radiation | Monochromator: single crystal Si(311) bent monochromator (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→49.32 Å / Num. all: 47751 / Num. obs: 47751 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 64.3 Å2 / Rsym value: 0.119 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 3.25→3.43 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 6920 / Rsym value: 0.45 / % possible all: 98.7 |
Reflection | *PLUS Num. measured all: 348873 / Rmerge(I) obs: 0.119 |
Reflection shell | *PLUS % possible obs: 98.8 % / Rmerge(I) obs: 0.45 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID Code 1AIJ and 1CXC are starting models for the reaction center and cytochrome c2 respectively. RESIDUES LISTED IN REMARK 465 ARE MISSING DUE TO LACK OF ELECTRON DENSITY. ATOMS ...Starting model: PDB ID Code 1AIJ and 1CXC are starting models for the reaction center and cytochrome c2 respectively. RESIDUES LISTED IN REMARK 465 ARE MISSING DUE TO LACK OF ELECTRON DENSITY. ATOMS ON THE ISOPRENOID TAIL OF BCL 1001 and 2001, BPH 1005 and 2005, AND U10 1008 and 2008 ARE MISSING DUE TO THE LACK OF ELECTRON DENSITY. Resolution: 3.25→49.32 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 74.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.25→49.32 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor all: 0.263 / Rfactor obs: 0.248 / Rfactor Rfree: 0.287 / Rfactor Rwork: 0.248 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.373 / Rfactor Rwork: 0.328 / Rfactor obs: 0.328 |