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- PDB-1ijd: Crystallographic Structure of the LH3 Complex from Rhodopseudomon... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ijd | ||||||
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Title | Crystallographic Structure of the LH3 Complex from Rhodopseudomonas acidophila strain 7050 | ||||||
![]() | (LIGHT-HARVESTING PROTEIN B-800/820, ...) x 2 | ||||||
![]() | PHOTOSYNTHESIS / Pigment-protein complex / alpha-helix apoproteins / intergral membrane protein / light harvesting | ||||||
Function / homology | ![]() 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 / membrane => GO:0016020 / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | McLuskey, K. / Prince, S.M. / Cogdell, R.J. / Isaacs, N.W. | ||||||
![]() | ![]() Title: The crystallographic structure of the B800-820 LH3 light-harvesting complex from the purple bacteria Rhodopseudomonas acidophila strain 7050. Authors: McLuskey, K. / Prince, S.M. / Cogdell, R.J. / Isaacs, N.W. #1: ![]() Title: Crystallization and Preliminary X-ray Crystallographic Analysis of the B800-820 Light-harvesting Complex from Rhodopseudomonas acidophila Strain 7050 Authors: McLuskey, K. / Prince, S.M. / Cogdell, R.J. / Isaacs, N.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.8 KB | Display | ![]() |
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PDB format | ![]() | 65.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.2 MB | Display | ![]() |
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Full document | ![]() | 3.3 MB | Display | |
Data in XML | ![]() | 28.8 KB | Display | |
Data in CIF | ![]() | 28.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1kzuS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-LIGHT-HARVESTING PROTEIN B-800/820, ... , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 5578.656 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: Photosynthetic purple bacteria / Source: (natural) ![]() #2: Protein/peptide | Mass: 4731.449 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: Photosynthetic purple bacteria / Source: (natural) ![]() |
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-Sugars , 2 types, 6 molecules ![](data/chem/img/RPA.gif)
![](data/chem/img/BOG.gif)
![](data/chem/img/BOG.gif)
#4: Sugar | #5: Sugar | |
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-Non-polymers , 2 types, 51 molecules ![](data/chem/img/BCL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-BCL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.89 Å3/Da / Density % sol: 74 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9.2 Details: potassium phosphate, benzamidine HCl, B-Octyl glucoside, sodium chloride, pH 9.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K | ||||||||||||||||||||||||
Crystal grow | *PLUS Details: McLuskey, K., (1999) Acta Crystallogr., Sect.D, 55, 885. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.8→42 Å / Num. obs: 18970 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 3.7 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 4.6 | ||||||||||||||||||
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.3 / % possible all: 94.7 | ||||||||||||||||||
Reflection | *PLUS Highest resolution: 3 Å / % possible obs: 97 % / Rmerge(I) obs: 0.085 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 96.4 % / Rmerge(I) obs: 0.37 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1KZU (LH2 complex from Rps. acidophila strain 10050) Resolution: 3→42 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 Stereochemistry target values: Engh & Huber for protein, for cofactors; geometry derived from small molecule structures
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Displacement parameters | Biso mean: 46.4 Å2 | ||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.36 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→42 Å
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LS refinement shell | Resolution: 3→3.19 Å
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Software | *PLUS Name: RESTRAIN / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å / σ(F): 2 / Rfactor obs: 0.243 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 46.4 Å2 | ||||||||||||||||||||
Refine LS restraints | *PLUS
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