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Yorodumi- PDB-2x5v: 80 microsecond laue diffraction snapshot from crystals of a photo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x5v | |||||||||
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Title | 80 microsecond laue diffraction snapshot from crystals of a photosynthetic reaction centre 3 millisecond following photoactivation. | |||||||||
Components |
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Keywords | PHOTOSYNTHESIS / LIPIDIC-SPONGE PHASE / ELECTRON TRANSPORT / CELL MEMBRANE / METAL-BINDING / TRANSMEMBRANE / FORMYLATION / LIPOPROTEIN / LIPIDS / TRANSPORT | |||||||||
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 | BLASTOCHLORIS VIRIDIS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Wohri, A.B. / Katona, G. / Johansson, L.C. / Fritz, E. / Malmerberg, E. / Andersson, M. / Vincent, J. / Eklund, M. / Cammarata, M. / Wulff, M. ...Wohri, A.B. / Katona, G. / Johansson, L.C. / Fritz, E. / Malmerberg, E. / Andersson, M. / Vincent, J. / Eklund, M. / Cammarata, M. / Wulff, M. / Davidsson, J. / Groenhof, G. / Neutze, R. | |||||||||
Citation | Journal: Science / Year: 2010 Title: Light-Induced Structural Changes in a Photosynthetic Reaction Center Caught by Laue Diffraction. Authors: Wohri, A.B. / Katona, G. / Johansson, L.C. / Fritz, E. / Malmerberg, E. / Andersson, M. / Vincent, J. / Eklund, M. / Cammarata, M. / Wulff, M. / Davidsson, J. / Groenhof, G. / Neutze, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x5v.cif.gz | 258.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x5v.ent.gz | 205.1 KB | Display | PDB format |
PDBx/mmJSON format | 2x5v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x5v_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 2x5v_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 2x5v_validation.xml.gz | 49.5 KB | Display | |
Data in CIF | 2x5v_validation.cif.gz | 64.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/2x5v ftp://data.pdbj.org/pub/pdb/validation_reports/x5/2x5v | HTTPS FTP |
-Related structure data
Related structure data | 2x5uC 2wjnS C: citing same article (ref.) S: Starting model for refinement |
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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
-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) BLASTOCHLORIS VIRIDIS (bacteria) / References: UniProt: P07173 |
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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) BLASTOCHLORIS VIRIDIS (bacteria) / References: UniProt: P06008 |
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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) BLASTOCHLORIS 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) BLASTOCHLORIS VIRIDIS (bacteria) / References: UniProt: P06010 |
-Non-polymers , 6 types, 14 molecules
#5: Chemical | ChemComp-HEC / #6: Chemical | ChemComp-BCB / #7: Chemical | #8: Chemical | ChemComp-FE2 / | #9: Chemical | ChemComp-MQ7 / | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 3.96 Å3/Da / Density % sol: 68.69 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.1 Details: MONOOLEIN WAS MIXED WITH 0.1M HEPES PH 8.1, 0.1% LDAO IN 60:40 (W/W) RATIO. THEN THE CUBIC PHASE WAS MIXED WITH 16% JEFFAMINE M600, 1M HEPES PH 8.1, 0.7M AMMONIUM SULFATE, 2.5% 1,2,3- ...Details: MONOOLEIN WAS MIXED WITH 0.1M HEPES PH 8.1, 0.1% LDAO IN 60:40 (W/W) RATIO. THEN THE CUBIC PHASE WAS MIXED WITH 16% JEFFAMINE M600, 1M HEPES PH 8.1, 0.7M AMMONIUM SULFATE, 2.5% 1,2,3-HEPTANETRIOL IN 1 TO 4 RATIO AND EQUILIBRATED UNTIL PHASE SEPARATION OCCURED. 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. |
-Data collection
Diffraction | Mean temperature: 293 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 0.8-1.1 | |||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 12, 2007 | |||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 3→46.2 Å / Num. obs: 40530 / % possible obs: 90.6 % / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Biso Wilson estimate: 43.16 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 10.4 | |||||||||
Reflection shell | Resolution: 3→3.14 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 6.9 / % possible all: 74.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WJN Resolution: 3→46.18 Å / Cor.coef. Fo:Fc: 0.754 / Cor.coef. Fo:Fc free: 0.69 / SU B: 24.481 / SU ML: 0.463 / Cross valid method: THROUGHOUT / ESU R Free: 0.509 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.619 Å2
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Refinement step | Cycle: LAST / Resolution: 3→46.18 Å
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Refine LS restraints |
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