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Yorodumi- PDB-4cas: Serial femtosecond crystallography structure of a photosynthetic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cas | ||||||||||||
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Title | Serial femtosecond crystallography structure of a photosynthetic reaction center | ||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / LIPIDIC-SPONGE PHASE / REACTION CENTER / ELECTRON TRANSPORT / CELL MEMBRANE / METAL- BINDING / TRANSMEMBRANE / CHROMOPHORE | ||||||||||||
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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||||||||
Authors | Johansson, L.C. / Arnlund, D. / Katona, G. / White, T.A. / Barty, A. / DePonte, D.P. / Shoeman, R.L. / Wickstrand, C. / Sharma, A. / Williams, G.J. ...Johansson, L.C. / Arnlund, D. / Katona, G. / White, T.A. / Barty, A. / DePonte, D.P. / Shoeman, R.L. / Wickstrand, C. / Sharma, A. / Williams, G.J. / Aquila, A. / Bogan, M.J. / Caleman, C. / Davidsson, J. / Doak, R.B. / Frank, M. / Fromme, R. / Galli, L. / Grotjohann, I. / Hunter, M.S. / Kassemeyer, S. / Kirian, R.A. / Kupitz, C. / Liang, M. / Lomb, L. / Malmerberg, E. / Martin, A.V. / Messerschmidt, M. / Nass, K. / Redecke, L. / Seibert, M.M. / Sjohamn, J. / Steinbrener, J. / Stellato, F. / Wang, D. / Wahlgren, W.Y. / Weierstall, U. / Westenhoff, S. / Zatsepin, N.A. / Boutet, S. / Spence, J.C.H. / Schlichting, I. / Chapman, H.N. / Fromme, P. / Neutze, R. | ||||||||||||
Citation | Journal: Nat Commun / Year: 2013 Title: Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography. Authors: Johansson, L.C. / Arnlund, D. / Katona, G. / White, T.A. / Barty, A. / DePonte, D.P. / Shoeman, R.L. / Wickstrand, C. / Sharma, A. / Williams, G.J. / Aquila, A. / Bogan, M.J. / Caleman, C. / ...Authors: Johansson, L.C. / Arnlund, D. / Katona, G. / White, T.A. / Barty, A. / DePonte, D.P. / Shoeman, R.L. / Wickstrand, C. / Sharma, A. / Williams, G.J. / Aquila, A. / Bogan, M.J. / Caleman, C. / Davidsson, J. / Doak, R.B. / Frank, M. / Fromme, R. / Galli, L. / Grotjohann, I. / Hunter, M.S. / Kassemeyer, S. / Kirian, R.A. / Kupitz, C. / Liang, M. / Lomb, L. / Malmerberg, E. / Martin, A.V. / Messerschmidt, M. / Nass, K. / Redecke, L. / Seibert, M.M. / Sjohamn, J. / Steinbrener, J. / Stellato, F. / Wang, D. / Wahlgren, W.Y. / Weierstall, U. / Westenhoff, S. / Zatsepin, N.A. / Boutet, S. / Spence, J.C. / Schlichting, I. / Chapman, H.N. / Fromme, P. / Neutze, R. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cas.cif.gz | 497 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cas.ent.gz | 404.2 KB | Display | PDB format |
PDBx/mmJSON format | 4cas.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cas_validation.pdf.gz | 3.6 MB | Display | wwPDB validaton report |
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Full document | 4cas_full_validation.pdf.gz | 3.8 MB | Display | |
Data in XML | 4cas_validation.xml.gz | 50.3 KB | Display | |
Data in CIF | 4cas_validation.cif.gz | 64.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/4cas ftp://data.pdbj.org/pub/pdb/validation_reports/ca/4cas | HTTPS FTP |
-Related structure data
Related structure data | 2wjnS 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 A
#1: Protein | Mass: 39419.176 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 BCD
#2: 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 |
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#3: 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 |
#4: 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 |
-Non-polymers , 10 types, 20 molecules
#5: Chemical | ChemComp-HEC / #6: Chemical | ChemComp-DGA / | #7: Chemical | ChemComp-BCL / #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-FE2 / | #11: Chemical | ChemComp-MQ7 / | #12: Chemical | ChemComp-NS5 / | #13: Chemical | ChemComp-OTP / ( | #14: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1175 |
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-Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.8 % Description: DATA WAS COLLECTED ON 1175 MICROCRYSTALS AT THE LCLS USING THE SERIAL FEMTOSECOND CRYSTALLOGRAPHY METHOD. |
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Crystal grow | pH: 8.1 Details: BATCH CRYSTALLIZATIONS WERE SET UP IN SEPTUM-SEALED GLASS VIALS CONTAINING 100 UL PROTEIN (30-35 MG/ML), 100 UL LIPIDIC SPONGE PHASE (12 % MONOOLEIN, 17.5 % JEFFAMINE M 600, 1.0 M HEPES PH 8. ...Details: BATCH CRYSTALLIZATIONS WERE SET UP IN SEPTUM-SEALED GLASS VIALS CONTAINING 100 UL PROTEIN (30-35 MG/ML), 100 UL LIPIDIC SPONGE PHASE (12 % MONOOLEIN, 17.5 % JEFFAMINE M 600, 1.0 M HEPES PH 8.0, 0.7 M (NH4)2SO4, 2.5 % 1,2,3- HEPTANETRIOL) AND 100 UL 1.0-1.2 M TRI-SODIUM CITRATE |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.32 / Wavelength: 1.32 Å |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Feb 19, 2011 / Details: BE LENSES |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.32 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→50 Å / Num. obs: 23496 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 27 % / CC1/2: 0.54 / R split: 0.365 / Net I/σ(I): 3.5 |
Reflection shell | Resolution: 3.5→3.59 Å / Redundancy: 26.6 % / Mean I/σ(I) obs: 2 / CC1/2: 0.32 / R split: 0.527 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WJN Resolution: 3.5→49.64 Å / Cor.coef. Fo:Fc: 0.731 / Cor.coef. Fo:Fc free: 0.645 / SU B: 86.357 / SU ML: 0.737 / Cross valid method: THROUGHOUT / ESU R Free: 0.763 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.177 Å2
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Refinement step | Cycle: LAST / Resolution: 3.5→49.64 Å
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Refine LS restraints |
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