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Yorodumi- PDB-2axt: Crystal Structure of Photosystem II from Thermosynechococcus elongatus -
+Open data
-Basic information
Entry | Database: PDB / ID: 2axt | |||||||||
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Title | Crystal Structure of Photosystem II from Thermosynechococcus elongatus | |||||||||
Components |
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Keywords | ELECTRON TRANSPORT / photosystem / ps ii / ps2 / membrane complex / transmembrane alpha-helix | |||||||||
Function / homology | Function and homology information photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / extrinsic component of membrane ...photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / extrinsic component of membrane / photosystem II / photosynthesis, light reaction / phosphate ion binding / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / respiratory electron transport chain / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Thermosynechococcus elongatus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3 Å | |||||||||
Authors | Loll, B. / Kern, J. / Saenger, W. / Zouni, A. / Biesiadka, J. | |||||||||
Citation | Journal: NATURE / Year: 2005 Title: Towards complete cofactor arrangement in the 3.0 A resolution structure of photosystem II Authors: Loll, B. / Kern, J. / Saenger, W. / Zouni, A. / Biesiadka, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2axt.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2axt.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 2axt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2axt_validation.pdf.gz | 24.9 MB | Display | wwPDB validaton report |
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Full document | 2axt_full_validation.pdf.gz | 25.4 MB | Display | |
Data in XML | 2axt_validation.xml.gz | 268.6 KB | Display | |
Data in CIF | 2axt_validation.cif.gz | 327.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/2axt ftp://data.pdbj.org/pub/pdb/validation_reports/ax/2axt | 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 , 4 types, 8 molecules AaBbVvXx
#1: Protein | Mass: 38265.625 Da / Num. of mol.: 2 / Fragment: residues 1-344 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: P0A445, UniProt: P0A444*PLUS #2: Protein | Mass: 56656.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: GenBank: 11761354, UniProt: Q8DIQ1*PLUS #16: Protein | Mass: 15148.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: P0A386 #17: Protein | Mass: 10996.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) |
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-Photosystem II ... , 12 types, 24 molecules CcDdHhIiJjKkLlMmOoTtUuZz
#3: Protein | Mass: 51666.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: GenBank: 22295356, UniProt: Q8DIF8*PLUS #4: Protein | Mass: 39388.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: GenBank: 22295355, UniProt: Q8CM25*PLUS #7: Protein | Mass: 7358.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8DJ43 #8: Protein/peptide | Mass: 4410.245 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8DJZ6 #9: Protein/peptide | Mass: 4105.908 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: P59087 #10: Protein/peptide | Mass: 4101.911 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q9F1K9 #11: Protein/peptide | Mass: 4299.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8DIN8 #12: Protein/peptide | Mass: 3981.673 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8DHA7 #13: Protein | Mass: 26923.045 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: P0A431 #14: Protein/peptide | Mass: 3878.728 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8DIQ0 #15: Protein | Mass: 11655.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q9F1L5 #18: Protein | Mass: 6766.187 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8DHJ2 |
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-Cytochrome b559 ... , 2 types, 4 molecules EeFf
#5: Protein | Mass: 9580.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8DIP0 #6: Protein/peptide | Mass: 5067.900 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8DIN9 |
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-Sugars , 2 types, 14 molecules
#27: Sugar | ChemComp-LMT / #30: Sugar | ChemComp-DGD / |
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-Non-polymers , 13 types, 166 molecules
#19: Chemical | #20: Chemical | ChemComp-CLA / #21: Chemical | ChemComp-PHO / #22: Chemical | ChemComp-PQ9 / #23: Chemical | #24: Chemical | ChemComp-BCR / #25: Chemical | #26: Chemical | ChemComp-SQD / #28: Chemical | ChemComp-MGE / ( #29: Chemical | ChemComp-UNK / #31: Chemical | #32: Chemical | ChemComp-HEM / #33: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.76 Å3/Da / Density % sol: 67.32 % |
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Crystal grow | Temperature: 298 K / Method: batch / pH: 7 Details: PEG 2000, PIPES, magnesium chloride, pH 7.0, batch, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 24, 2005 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 155380 / % possible obs: 88.2 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rsym value: 0.103 / Net I/σ(I): 14.83 |
Reflection shell | Resolution: 3→3.05 Å / Mean I/σ(I) obs: 2.17 / Rsym value: 0.466 / % possible all: 73.3 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 3→10 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 4628278.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.6527 Å2 / ksol: 0.303343 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→10 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.18 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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