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Yorodumi- PDB-1l9b: X-Ray Structure of the Cytochrome-c(2)-Photosynthetic Reaction Ce... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l9b | ||||||
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Title | X-Ray Structure of the Cytochrome-c(2)-Photosynthetic Reaction Center Electron Transfer Complex from Rhodobacter sphaeroides in Type II Co-Crystals | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / bacterial photosynthesis / protein-protein interaction / electron transfer proteins / membrane proteins / protein complexes | ||||||
Function / homology | Function and homology information : / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / electron transfer activity / periplasmic space ...: / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / electron transfer activity / periplasmic space / membrane => GO:0016020 / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodobacter sphaeroides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 | 1l9b.cif.gz | 223.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l9b.ent.gz | 173.4 KB | Display | PDB format |
PDBx/mmJSON format | 1l9b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/1l9b ftp://data.pdbj.org/pub/pdb/validation_reports/l9/1l9b | HTTPS FTP |
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-Related structure data
Related structure data | 1l9jC 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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Unit cell |
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-Components
-REACTION CENTER PROTEIN ... , 3 types, 3 molecules LMH
#1: Protein | Mass: 31346.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R26 / References: UniProt: P02954, UniProt: P0C0Y8*PLUS |
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#2: Protein | Mass: 34398.543 Da / Num. of mol.: 1 / 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.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R26 / References: UniProt: P11846, UniProt: P0C0Y7*PLUS |
-Protein , 1 types, 1 molecules C
#4: Protein | Mass: 13488.064 Da / Num. of mol.: 1 / 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 , 10 types, 307 molecules
#5: Chemical | ChemComp-NA / | ||||||||||||||||
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#6: Chemical | ChemComp-BCL / #7: Chemical | #8: Chemical | ChemComp-LDA / #9: Chemical | #10: Chemical | ChemComp-FE2 / | #11: Chemical | ChemComp-CL / | #12: Chemical | ChemComp-U10 / | #13: Chemical | ChemComp-HEM / | #14: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.94 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 10% PEG 4000, 0.06%(w/v) lauryldimethylamine-N-oxide, 3.9%(w/v) heptane-1,2,3-triol, 15 mM Tricine, 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: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 18, 2001 |
Radiation | Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→45.73 Å / Num. all: 50331 / Num. obs: 50331 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 63.2 Å2 / Rsym value: 0.1 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 6325 / Rsym value: 0.326 / % possible all: 83.7 |
Reflection | *PLUS Num. measured all: 196158 / Rmerge(I) obs: 0.1 |
Reflection shell | *PLUS % possible obs: 83.7 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 2 |
-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. Resolution: 2.4→45.73 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Residues listed in remark 465 are missing due to lack of electron density. Atoms on the isoprenoid tail of BCL 1001, BPH 1005, and U10 1008 are missing due to the lack of electron density. ...Details: Residues listed in remark 465 are missing due to lack of electron density. Atoms on the isoprenoid tail of BCL 1001, BPH 1005, and U10 1008 are missing due to the lack of electron density. The 3.6 Angstrom distance between the sidechains of Lys C10 and Asp M292 cannot be corroborated because of the lack of complete sidechain electron density for Lys C10.
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Displacement parameters | Biso mean: 61.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→45.73 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: 10
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Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor obs: 0.22 / Rfactor Rfree: 0.264 / Rfactor Rwork: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.4466 / Rfactor Rwork: 0.4311 / Rfactor obs: 0.4311 |