+Open data
-Basic information
Entry | Database: PDB / ID: 3pcq | |||||||||
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Title | Femtosecond X-ray protein Nanocrystallography | |||||||||
Components | (Photosystem I ...) x 12 | |||||||||
Keywords | PHOTOSYNTHESIS / MEMBRANE PROTEIN / MULTIPROTEIN-PIGMENT COMPLEX | |||||||||
Function / homology | Function and homology information photosystem I reaction center / photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthetic electron transport in photosystem I / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity ...photosystem I reaction center / photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthetic electron transport in photosystem I / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Thermosynechococcus elongatus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 8.984 Å | |||||||||
Authors | Chapman, H.N. / Fromme, P. / Barty, A. / White, T.A. / Kirian, R.A. / Aquila, A. / Hunter, M.S. / Schulz, J. / Deponte, D.P. / Weierstall, U. ...Chapman, H.N. / Fromme, P. / Barty, A. / White, T.A. / Kirian, R.A. / Aquila, A. / Hunter, M.S. / Schulz, J. / Deponte, D.P. / Weierstall, U. / Doak, R.B. / Maia, F.R.N.C. / Martin, A.V. / Schlichting, I. / Lomb, L. / Coppola, N. / Shoeman, R.L. / Epp, S.W. / Hartmann, R. / Rolles, D. / Rudenko, A. / Foucar, L. / Kimmel, N. / Weidenspointner, G. / Holl, P. / Liang, M. / Barthelmess, M. / Caleman, C. / Boutet, S. / Bogan, M.J. / Krzywinski, J. / Bostedt, C. / Bajt, S. / Gumprecht, L. / Rudek, B. / Erk, B. / Schmidt, C. / Homke, A. / Reich, C. / Pietschner, D. / Struder, L. / Hauser, G. / Gorke, H. / Ullrich, J. / Herrmann, S. / Schaller, G. / Schopper, F. / Soltau, H. / Kuhnel, K.-U. / Messerschmidt, M. / Bozek, J.D. / Hau-Riege, S.P. / Frank, M. / Hampton, C.Y. / Sierra, R. / Starodub, D. / Williams, G.J. / Hajdu, J. / Timneanu, N. / Seibert, M.M. / Andreasson, J. / Rocker, A. / Jonsson, O. / Svenda, M. / Stern, S. / Nass, K. / Andritschke, R. / Schroter, C.-D. / Krasniqi, F. / Bott, M. / Schmidt, K.E. / Wang, X. / Grotjohann, I. / Holton, J.M. / Barends, T.R.M. / Neutze, R. / Marchesini, S. / Fromme, R. / Schorb, S. / Rupp, D. / Adolph, M. / Gorkhover, T. / Andersson, I. / Hirsemann, H. / Potdevin, G. / Graafsma, H. / Nilsson, B. / Spence, J.C.H. | |||||||||
Citation | Journal: Nature / Year: 2011 Title: Femtosecond X-ray protein nanocrystallography. Authors: Chapman, H.N. / Fromme, P. / Barty, A. / White, T.A. / Kirian, R.A. / Aquila, A. / Hunter, M.S. / Schulz, J. / Deponte, D.P. / Weierstall, U. / Doak, R.B. / Maia, F.R. / Martin, A.V. / ...Authors: Chapman, H.N. / Fromme, P. / Barty, A. / White, T.A. / Kirian, R.A. / Aquila, A. / Hunter, M.S. / Schulz, J. / Deponte, D.P. / Weierstall, U. / Doak, R.B. / Maia, F.R. / Martin, A.V. / Schlichting, I. / Lomb, L. / Coppola, N. / Shoeman, R.L. / Epp, S.W. / Hartmann, R. / Rolles, D. / Rudenko, A. / Foucar, L. / Kimmel, N. / Weidenspointner, G. / Holl, P. / Liang, M. / Barthelmess, M. / Caleman, C. / Boutet, S. / Bogan, M.J. / Krzywinski, J. / Bostedt, C. / Bajt, S. / Gumprecht, L. / Rudek, B. / Erk, B. / Schmidt, C. / Homke, A. / Reich, C. / Pietschner, D. / Struder, L. / Hauser, G. / Gorke, H. / Ullrich, J. / Herrmann, S. / Schaller, G. / Schopper, F. / Soltau, H. / Kuhnel, K.U. / Messerschmidt, M. / Bozek, J.D. / Hau-Riege, S.P. / Frank, M. / Hampton, C.Y. / Sierra, R.G. / Starodub, D. / Williams, G.J. / Hajdu, J. / Timneanu, N. / Seibert, M.M. / Andreasson, J. / Rocker, A. / Jonsson, O. / Svenda, M. / Stern, S. / Nass, K. / Andritschke, R. / Schroter, C.D. / Krasniqi, F. / Bott, M. / Schmidt, K.E. / Wang, X. / Grotjohann, I. / Holton, J.M. / Barends, T.R. / Neutze, R. / Marchesini, S. / Fromme, R. / Schorb, S. / Rupp, D. / Adolph, M. / Gorkhover, T. / Andersson, I. / Hirsemann, H. / Potdevin, G. / Graafsma, H. / Nilsson, B. / Spence, J.C. #1: Journal: Nature / Year: 2001 Title: Three-dimensional structure of cyanobacterial photosystem I at 2.5 A resolution Authors: Jordan, P. / Fromme, P. / Witt, H.T. / Klukas, O. / Saenger, W. / Krauss, N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pcq.cif.gz | 629.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pcq.ent.gz | 537.9 KB | Display | PDB format |
PDBx/mmJSON format | 3pcq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pc/3pcq ftp://data.pdbj.org/pub/pdb/validation_reports/pc/3pcq | HTTPS FTP |
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-Related structure data
Related structure data | 1jb0S 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
-Photosystem I ... , 12 types, 12 molecules ABCDEFIJKLMX
#1: Protein | Mass: 83267.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A405 |
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#2: Protein | Mass: 82992.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A407 |
#3: Protein | Mass: 8678.011 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A415 |
#4: Protein | Mass: 15258.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A420 |
#5: Protein | Mass: 8268.290 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A423 |
#6: Protein | Mass: 17716.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A401 |
#7: Protein/peptide | Mass: 4297.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A427 |
#8: Protein/peptide | Mass: 4770.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A429 |
#9: Protein | Mass: 8483.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A425 |
#10: Protein | Mass: 16156.569 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DGB4 |
#11: Protein/peptide | Mass: 3426.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A403 |
#12: Protein/peptide | Mass: 3973.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DKP6 |
-Non-polymers , 8 types, 328 molecules
#13: Chemical | ChemComp-CLA / #14: Chemical | #15: Chemical | #16: Chemical | ChemComp-BCR / #17: Chemical | #18: Chemical | ChemComp-LMG / | #19: Chemical | ChemComp-CA / | #20: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 15445 |
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-Sample preparation
Crystal grow | Temperature: 277 K / pH: 6.4 Details: 0.008 M MAGNESIUM SULFATE, 0.005 M MES PH 6.4, 0.02% BETA-DODECYLMALTOSIDE, Batch nanocrystallization, temperature 277K |
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-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection twin |
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Reflection | Resolution: 8.66→243.47 Å / Num. all: 6677 / Num. obs: 6111 / % possible obs: 91.52 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 738 % / Net I/σ(I): 11.11 | ||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1JB0 Resolution: 8.984→81.12 Å / Cor.coef. Fo:Fc: 0.777 / Cor.coef. Fo:Fc free: 0.758 / SU B: 571.44 / SU ML: 3.653 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.973 / Stereochemistry target values: Engh & Huber / 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: MASK | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.257 Å2
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Refinement step | Cycle: LAST / Resolution: 8.984→81.12 Å
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LS refinement shell | Resolution: 8.984→9.217 Å / Total num. of bins used: 20
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