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- PDB-2wjm: Lipidic sponge phase crystal structure of the photosynthetic reac... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wjm | ||||||||||||
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Title | Lipidic sponge phase crystal structure of the photosynthetic reaction centre from Blastochloris viridis (low dose) | ||||||||||||
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![]() | PHOTOSYNTHESIS / REACTION CENTRE / MEMBRANE PROTEIN / LIPIDS / MONOOLEIN / POSTTRANSLATIONAL MODIFICATION / THIOETHER BOND / UBIQUINONE / LIPIDIC SPONGE PHASE | ||||||||||||
Function / homology | ![]() 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 / electron transfer activity / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Woehri, A.B. / Wahlgren, W.Y. / Malmerberg, E. / Johansson, L.C. / Neutze, R. / Katona, G. | ||||||||||||
![]() | ![]() Title: Lipidic sponge phase crystal structure of a photosynthetic reaction center reveals lipids on the protein surface. Authors: Wohri, A.B. / Wahlgren, W.Y. / Malmerberg, E. / Johansson, L.C. / Neutze, R. / Katona, G. | ||||||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 285.7 KB | Display | ![]() |
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PDB format | ![]() | 222.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2wjnC ![]() 2prcS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules C
#1: Protein | Mass: 37450.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: DEUTSCHE SAMMLUNG VON MIKROORGANISMEN UND ZELLKULTUREN GMBH (DSMZ) Source: (natural) ![]() |
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-REACTION CENTER PROTEIN ... , 3 types, 3 molecules HLM
#2: Protein | Mass: 28557.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: DEUTSCHE SAMMLUNG VON MIKROORGANISMEN UND ZELLKULTUREN GMBH (DSMZ) Source: (natural) ![]() |
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#3: Protein | Mass: 30600.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: DEUTSCHE SAMMLUNG VON MIKROORGANISMEN UND ZELLKULTUREN GMBH (DSMZ) Source: (natural) ![]() |
#4: Protein | Mass: 36063.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: DEUTSCHE SAMMLUNG VON MIKROORGANISMEN UND ZELLKULTUREN GMBH (DSMZ) Source: (natural) ![]() |
-Non-polymers , 10 types, 730 molecules ![](data/chem/img/HEC.gif)
![](data/chem/img/DGA.gif)
![](data/chem/img/BCB.gif)
![](data/chem/img/BPB.gif)
![](data/chem/img/MPG.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/MQ7.gif)
![](data/chem/img/NS5.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DGA.gif)
![](data/chem/img/BCB.gif)
![](data/chem/img/BPB.gif)
![](data/chem/img/MPG.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/MQ7.gif)
![](data/chem/img/NS5.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-HEC / #6: Chemical | ChemComp-DGA / | #7: Chemical | ChemComp-BCB / #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-FE2 / | #11: Chemical | ChemComp-MQ7 / | #12: Chemical | ChemComp-NS5 / | #13: Chemical | #14: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | DIACYL GLYCEROL (DGA): THIOETHER BOND THROUGH C1 CYS -H2O PROTOPORPHYRIN IX CONTAINING FE (HEM): ...DIACYL GLYCEROL (DGA): THIOETHER BOND THROUGH C1 CYS -H2O PROTOPORPH |
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Sequence details | N-TERMINUS IS PROCESSED BY A SIGNAL PEPTIDASE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | Method: lipidic cubic phase / pH: 8 Details: MONOOLEIN WAS MIXED WITH WATER IN RATIO OF 60:40 (W/W) UNTIL A VISCOUS NON-BIREFRINGENT LCP WAS FORMED. THEREAFTER, LIPIDIC-SPONGE PHASE INITIATING SOLUTION (20% JEFFAMINE M600, 1M HEPES ...Details: MONOOLEIN WAS MIXED WITH WATER IN RATIO OF 60:40 (W/W) UNTIL A VISCOUS NON-BIREFRINGENT LCP WAS FORMED. THEREAFTER, LIPIDIC-SPONGE PHASE INITIATING SOLUTION (20% JEFFAMINE M600, 1M HEPES PH=8.0, 0.7M (NH4)2SO4 AND 2.5% 1,2,3-HEPTANETRIOL) WAS ADDED IN A RATIO OF 1 TO 4 (V/V) AND EQUILIBRATED UNTIL PHASE SEPARATION HAS OCCURRED. THE UPPER LIPIDIC-SPONGE PHASE WAS HARVESTED AND 1UL WAS USED AS A PRECIPITANT SOLUTION TOGETHER WITH 1UL OF 25 MG/ML PROTEIN SOLUTION IN A HANGING-DROP, VAPOUR-DIFFUSION EXPERIMENT. TO IMPROVE CRYSTAL QUALITY 1UL OF ADDITIVE 1M TRI-NA-CITRATE HAS BEEN ADDED TO THE CRYSTALLIZATION DROP. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 8, 2007 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND (111), GE (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→45.9 Å / Num. obs: 152112 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.1 / % possible all: 86.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2PRC Resolution: 1.95→176.78 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.567 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.466 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→176.78 Å
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Refine LS restraints |
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