[English] 日本語
Yorodumi- PDB-2wjn: Lipidic sponge phase crystal structure of photosynthetic reaction... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wjn | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Lipidic sponge phase crystal structure of photosynthetic reaction centre from Blastochloris viridis (high dose) | ||||||||||||
Components |
| ||||||||||||
Keywords | PHOTOSYNTHESIS / BACTERIOCHLOROPHYLL / LIPIDIC-SPONGE PHASE / REACTION CENTER / ELECTRON TRANSPORT / CELL MEMBRANE / METAL-BINDING / TRANSMEMBRANE / FORMYLATION / CHROMOPHORE / CHLOROPHYLL / LIPOPROTEIN / IRON / HEME / LIPIDS / MEMBRANE / TRANSPORT / MAGNESIUM | ||||||||||||
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 / electron transfer activity / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | RHODOPSEUDOMONAS VIRIDIS (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||||||||
Authors | Wohri, A.B. / Wahlgren, W.Y. / Malmerberg, E. / Johansson, L.C. / Neutze, R. / Katona, G. | ||||||||||||
Citation | Journal: Biochemistry / Year: 2009 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 |
| ||||||||||||
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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2wjn.cif.gz | 284.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2wjn.ent.gz | 221 KB | Display | PDB format |
PDBx/mmJSON format | 2wjn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wjn_validation.pdf.gz | 4.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2wjn_full_validation.pdf.gz | 4.3 MB | Display | |
Data in XML | 2wjn_validation.xml.gz | 57.2 KB | Display | |
Data in CIF | 2wjn_validation.cif.gz | 80.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/2wjn ftp://data.pdbj.org/pub/pdb/validation_reports/wj/2wjn | HTTPS FTP |
-Related structure data
Related structure data | 2wjmC 2prcS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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) RHODOPSEUDOMONAS VIRIDIS (bacteria) / References: UniProt: P07173 |
---|
-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) RHODOPSEUDOMONAS VIRIDIS (bacteria) / References: UniProt: P06008 |
---|---|
#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) RHODOPSEUDOMONAS VIRIDIS (bacteria) / References: UniProt: P06009 |
#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) RHODOPSEUDOMONAS VIRIDIS (bacteria) / References: UniProt: P06010 |
-Non-polymers , 8 types, 708 molecules
#5: Chemical | ChemComp-HEC / #6: Chemical | ChemComp-BCB / #7: Chemical | #8: Chemical | #9: Chemical | ChemComp-FE2 / | #10: Chemical | ChemComp-MQ7 / | #11: Chemical | ChemComp-NS5 / | #12: Water | ChemComp-HOH / | |
---|
-Details
Nonpolymer details | PROTOPORPHYRIN IX CONTAINING FE (HEM): COVALENTLY BONDED TO CYSTENES ...PROTOPORPH |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 54 % / Description: NONE |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9923 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2008 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9923 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→44.99 Å / Num. obs: 176119 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 6.55 % / Biso Wilson estimate: 32.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.97 |
Reflection shell | Resolution: 1.85→2 Å / Redundancy: 6.74 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.72 / % possible all: 92.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PRC Resolution: 1.86→44.97 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.749 / SU ML: 0.065 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.528 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→44.97 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|