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Yorodumi- PDB-4fe1: Improving the Accuracy of Macromolecular Structure Refinement at ... -
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-Basic information
Entry | Database: PDB / ID: 4fe1 | |||||||||
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Title | Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution | |||||||||
Components | (Photosystem I ...) x 12 | |||||||||
Keywords | PHOTOSYNTHESIS / photosystem / membrane protein / chlorophyll / chromophore / electron transport / metal-binding / photosystem I / thylakoid / transmembrane / electron transfer / membrane / thylakoidmembrane | |||||||||
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 / oxidoreductase activity / electron transfer 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 / oxidoreductase activity / electron transfer activity / magnesium ion binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Thermosynechococcus elongatus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.9228 Å | |||||||||
Authors | Fromme, R. / Adams, P.D. / Fromme, P. / Levitt, M. / Schroeder, G.F. / Brunger, A.T. | |||||||||
Citation | Journal: Structure / Year: 2012 Title: Improving the accuracy of macromolecular structure refinement at 7 A resolution. Authors: Brunger, A.T. / Adams, P.D. / Fromme, P. / Fromme, R. / Levitt, M. / Schroder, G.F. #1: 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. #2: 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. #3: Journal: Nature / Year: 2010 Title: Super-resolution biomolecular crystallography with low-resolution data. Authors: Schroder, G.F. / Levitt, M. / Brunger, A.T. #4: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010 Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution. Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart / Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fe1.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4fe1.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 4fe1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fe1_validation.pdf.gz | 22.3 MB | Display | wwPDB validaton report |
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Full document | 4fe1_full_validation.pdf.gz | 22.8 MB | Display | |
Data in XML | 4fe1_validation.xml.gz | 155.5 KB | Display | |
Data in CIF | 4fe1_validation.cif.gz | 189.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/4fe1 ftp://data.pdbj.org/pub/pdb/validation_reports/fe/4fe1 | HTTPS FTP |
-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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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, photosystem I |
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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, photosystem I |
#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, photosystem I |
#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: 3845.508 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 , 7 types, 128 molecules
#13: Chemical | ChemComp-CLA / #14: Chemical | #15: Chemical | ChemComp-BCR / #16: Chemical | #17: Chemical | #18: Chemical | ChemComp-LMG / | #19: Chemical | ChemComp-CA / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 7.32 Å3/Da / Density % sol: 83.2 % |
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Crystal grow | Temperature: 277 K / Method: microdialysis / pH: 6.4 Details: beta-dodecylmaltoside, magnesium sulfate, pH 6.4, MICRODIALYSIS, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 16, 2010 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 4.9→247.463 Å / Num. all: 33699 / Num. obs: 33699 / % possible obs: 97.59 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JB0 Resolution: 4.9228→97.971 Å / SU ML: 0.83 / σ(F): 0 / Phase error: 31.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.9228→97.971 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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