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Yorodumi- PDB-1lgh: CRYSTAL STRUCTURE OF THE LIGHT-HARVESTING COMPLEX II (B800-850) F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lgh | ||||||
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Title | CRYSTAL STRUCTURE OF THE LIGHT-HARVESTING COMPLEX II (B800-850) FROM RHODOSPIRILLUM MOLISCHIANUM | ||||||
Components | (LIGHT HARVESTING COMPLEX ...Light-harvesting complex) x 2 | ||||||
Keywords | LIGHT HARVESTING COMPLEX / BACTERIOCHLOROPHYLL / DEXTER ENERGY TRANSFER / FOERSTER EXCITON TRANSFER MECHANISM / MEMBRANE PROTEIN / PHOTOSYNTHESIS | ||||||
Function / homology | Function and homology information organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Phaeospirillum molischianum (magnetotactic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Koepke, J. / Hu, X. / Schulten, K. / Michel, H. | ||||||
Citation | Journal: Structure / Year: 1996 Title: The crystal structure of the light-harvesting complex II (B800-850) from Rhodospirillum molischianum. Authors: Koepke, J. / Hu, X. / Muenke, C. / Schulten, K. / Michel, H. #1: Journal: Protein Sci. / Year: 1995 Title: Predicting the Structure of the Light-Harvesting Complex II of Rhodospirillum Molischianum Authors: Hu, X. / Xu, D. / Hamer, K. / Schulten, K. / Koepke, J. / Michel, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lgh.cif.gz | 147.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lgh.ent.gz | 124 KB | Display | PDB format |
PDBx/mmJSON format | 1lgh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/1lgh ftp://data.pdbj.org/pub/pdb/validation_reports/lg/1lgh | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE DEPOSITOR PROVIDED ONE ALPHA CHAIN, ONE BETA CHAIN, AND ASSOCIATED HET GROUPS AND WATERS. USING THE TRANSFORMATIONS ON MTRIX RECORDS BELOW, THE PDB GENERATED THE COMPLETE ASYMMETRIC UNIT, CONSISTING OF FOUR ALPHA CHAINS, FOUR BETA CHAINS, AND ASSOCIATED HET GROUPS AND WATERS. ALPHA AND BETA CHAINS HET GROUPS AND WATERS A, B C D, E F G, H I J, K L |
-Components
-LIGHT HARVESTING COMPLEX ... , 2 types, 8 molecules ADGJBEHK
#1: Protein | Mass: 5944.980 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) Phaeospirillum molischianum (magnetotactic) Strain: DSM 119 / References: UniProt: P97253 #2: Protein/peptide | Mass: 5120.873 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) Phaeospirillum molischianum (magnetotactic) Strain: DSM 119 / References: UniProt: P95673 |
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-Non-polymers , 5 types, 116 molecules
#3: Chemical | ChemComp-BCL / #4: Chemical | ChemComp-LYC / #5: Chemical | ChemComp-DET / #6: Chemical | ChemComp-HTO / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.97 Å3/Da / Density % sol: 70.7 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.009 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 8, 1989 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.009 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 31941 / % possible obs: 89.1 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.097 |
Reflection shell | Resolution: 2.4→2.59 Å / Rmerge(I) obs: 0.311 / % possible all: 66.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AS A SEARCH MODEL FOR MOLECULAR REPLACEMENT SERVED A COMPUTATIONALLY MODELLED OCTAMER OF ALPHA,BETA-HETERODIMERS BASED ON A HOMOLOGY OF THE LATTER TO THE ALPHA,BETA-HETERODIMER FROM RPS. ACIDOPHILA. Resolution: 2.4→8 Å / σ(F): 2
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Displacement parameters | Biso mean: 47 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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