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- PDB-5g3a: PsbO subunit of Photosystem II, beta barrel domain at 100K, pH 10 -
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Open data
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Basic information
Entry | Database: PDB / ID: 5g3a | ||||||
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Title | PsbO subunit of Photosystem II, beta barrel domain at 100K, pH 10 | ||||||
![]() | PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE | ||||||
![]() | PHOTOSYNTHESIS / CARBOXYLATE CLUSTER / PH / PROTON ANTENNA | ||||||
Function / homology | ![]() photosystem II assembly / photosystem II oxygen evolving complex / oxygen evolving activity / photosystem II stabilization / plasma membrane-derived thylakoid membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bommer, M. / Bondar, A.N. / Zouni, A. / Dobbek, H. / Dau, H. | ||||||
![]() | ![]() Title: Crystallographic and Computational Analysis of the Barrel Part of the Psbo Protein of Photosystem II -Carboxylate-Water Clusters as Putative Proton Transfer Relays and Structural Switches Authors: Bommer, M. / Bondar, A.N. / Zouni, A. / Dobbek, H. / Dau, H. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119.1 KB | Display | ![]() |
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PDB format | ![]() | 94.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422 KB | Display | ![]() |
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Full document | ![]() | 423.3 KB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 14.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5g38C ![]() 5g39C ![]() 3wu2S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 18621.721 Da / Num. of mol.: 1 / Fragment: BETA BARREL DOMAIN, RESIDUES 45-272 Source method: isolated from a genetically manipulated source Details: LOOPS 55-63,149-192 AND 220-231 DELETED Source: (gene. exp.) ![]() ![]() Strain: BP-1 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
Sequence details | LOOPS 55-63, 149-192 AND 220-231 REPLACED WITH A BETA HAIRPIN OF SEQUENCE NG |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.3 % / Description: NONE |
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Crystal grow | Method: vapor diffusion / pH: 10 Details: VAPOR DIFFUSION 30 MG/ML PROTEIN, 0.1 M MES-NA PH 6, 0.2 M CALCIUM ACETATE, 30% PEG 400, 0.01 M TCEP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2015 / Details: MIRRORS |
Radiation | Monochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→45.99 Å / Num. obs: 51297 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 18.8 % / Biso Wilson estimate: 12.99 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.57 |
Reflection shell | Resolution: 1.22→1.27 Å / Redundancy: 17.9 % / Mean I/σ(I) obs: 1.73 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3WU2 Resolution: 1.224→45.994 Å / SU ML: 0.11 / σ(F): 1.36 / Phase error: 17.57 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.224→45.994 Å
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Refine LS restraints |
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LS refinement shell |
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