+Open data
-Basic information
Entry | Database: PDB / ID: 1fe1 | ||||||
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Title | CRYSTAL STRUCTURE PHOTOSYSTEM II | ||||||
Components | (PROTEIN (PHOTOSYSTEM II: SUBUNIT ...) x 9 | ||||||
Keywords | PHOTOSYNTHESIS/ELECTRON TRANSPORT / PHOTOSYNTHESIS / PHOTOSYNTHETIC REACTION CENTER / CORE- ANTEN A LIGHT-HARVESTING SYSTEM / THERMOPHILIC CYANOBACTERIUM / MEMBRANE PROTEIN / PHOTOSYNTHESIS-ELECTRON TRANSPORT COMPLEX | ||||||
Function / homology | : / CHLOROPHYLL A / : / PROTOPORPHYRIN IX CONTAINING FE / : / PHEOPHYTIN A / Chem-PLA / TYROSINE Function and homology information | ||||||
Biological species | Synechococcus elongatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.8 Å | ||||||
Authors | Zouni, A. / Witt, H.-T. / Kern, J. / Fromme, P. / Krauss, N. / Saenger, W. / Orth, P. | ||||||
Citation | Journal: Nature / Year: 2001 Title: Crystal structure of photosystem II from Synechococcus elongatus at 3.8 A resolution. Authors: Zouni, A. / Witt, H.T. / Kern, J. / Fromme, P. / Krauss, N. / Saenger, W. / Orth, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fe1.cif.gz | 136.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fe1.ent.gz | 100.5 KB | Display | PDB format |
PDBx/mmJSON format | 1fe1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fe1_validation.pdf.gz | 3.9 MB | Display | wwPDB validaton report |
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Full document | 1fe1_full_validation.pdf.gz | 4.1 MB | Display | |
Data in XML | 1fe1_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 1fe1_validation.cif.gz | 35.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/1fe1 ftp://data.pdbj.org/pub/pdb/validation_reports/fe/1fe1 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-PROTEIN (PHOTOSYSTEM II: SUBUNIT ... , 9 types, 18 molecules AJBKCLDMENFOGPHQIR
#1: Protein | Mass: 14400.733 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANE #2: Protein | Mass: 14826.253 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANE #3: Protein | Mass: 13294.380 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANE #4: Protein | Mass: 13209.274 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANE #5: Protein/peptide | Mass: 3422.209 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANE #6: Protein/peptide | Mass: 2571.161 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANE #7: Protein | Mass: 26570.598 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANE #8: Protein | Mass: 9805.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANE, LUMEN #9: Protein | Mass: 7422.140 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANE, LUMEN |
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-Non-polymers , 8 types, 90 molecules
#10: Chemical | ChemComp-MN / #11: Chemical | ChemComp-TYR / #12: Chemical | ChemComp-CLA / #13: Chemical | ChemComp-PHO / #14: Chemical | #15: Chemical | #16: Chemical | ChemComp-HEM / #17: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 50 |
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-Sample preparation
Crystal | Density % sol: 45 % |
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Crystal grow | Temperature: 293 K / Method: batch method / pH: 7 Details: POLYETHYLENGLYCOL 2000, HEPES-BUFFER, CACL2 , pH 7.00, BATCH METHOD, temperature 293K |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | |||||||||||||||||||||||||
Reflection | Resolution: 3.8→20 Å / Num. all: 84964 / Num. obs: 84964 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 102 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 17.1 | |||||||||||||||||||||||||
Reflection shell | Resolution: 3.8→3.91 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.418 / % possible all: 84.5 | |||||||||||||||||||||||||
Reflection | *PLUS Highest resolution: 3.8 Å / Lowest resolution: 20 Å / Observed criterion σ(I): 0 / Redundancy: 3.2 % | |||||||||||||||||||||||||
Reflection shell | *PLUS % possible obs: 84.5 % / Mean I/σ(I) obs: 3.4 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 3.8→20 Å Details: THE STRUCTURE WAS SOLVED TO A RESOLUTION OF 4.2 ANGSTROEM USING 6 HEAVY ATOM DERIVATIVES. FOR DETAILS SEE ZOUNI ET AL. THE CADIMIUM DERIVATIVE HAS A RESOLUTION OF 3.8 ANGSTROEM. ...Details: THE STRUCTURE WAS SOLVED TO A RESOLUTION OF 4.2 ANGSTROEM USING 6 HEAVY ATOM DERIVATIVES. FOR DETAILS SEE ZOUNI ET AL. THE CADIMIUM DERIVATIVE HAS A RESOLUTION OF 3.8 ANGSTROEM. PHASEEXTENSION FROM 4.2 TILL 3.8 ANGSTROEM WAS PERFORMED USING TWO-FOLD NONCRYSTALLOGRAPHIC SYMMETRY AND SOLVENT FLATTENING. | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.8→20 Å
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Refinement | *PLUS Rfactor obs: 0.59 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |