+Open data
-Basic information
Entry | Database: PDB / ID: 5g38 | |||||||||
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Title | PsbO subunit of Photosystem II, beta barrel domain at 100K, pH 6 | |||||||||
Components | PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE | |||||||||
Keywords | PHOTOSYNTHESIS / CARBOXYLATE CLUSTER / PH / PROTON ANTENNA | |||||||||
Function / homology | Function and homology information photosystem II assembly / photosystem II oxygen evolving complex / oxygen evolving activity / photosystem II stabilization / plasma membrane-derived thylakoid membrane Similarity search - Function | |||||||||
Biological species | THERMOSYNECHOCOCCUS ELONGATUS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | |||||||||
Authors | Bommer, M. / Bondar, A.N. / Zouni, A. / Dobbek, H. / Dau, H. | |||||||||
Citation | Journal: Biochemistry / Year: 2016 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: AUTHOR PROVIDED.REMARK 800 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g38.cif.gz | 121.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g38.ent.gz | 96.8 KB | Display | PDB format |
PDBx/mmJSON format | 5g38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5g38_validation.pdf.gz | 427.8 KB | Display | wwPDB validaton report |
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Full document | 5g38_full_validation.pdf.gz | 430.2 KB | Display | |
Data in XML | 5g38_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 5g38_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/5g38 ftp://data.pdbj.org/pub/pdb/validation_reports/g3/5g38 | HTTPS FTP |
-Related structure data
Related structure data | 5g39C 5g3aC 3wu2S C: citing same article (ref.) 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 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.) THERMOSYNECHOCOCCUS ELONGATUS (bacteria) Strain: BP-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A432 | ||||
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#2: Chemical | #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: 6 Details: VAPOR DIFFUSION 30 MG/ML PSBO, 0.05 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: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 |
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: 1.15→26.45 Å / Num. obs: 60817 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 18.6 % / Biso Wilson estimate: 13.55 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 1.15→1.19 Å / Redundancy: 18 % / Rmerge(I) obs: 1.3 / Mean I/σ(I) obs: 2.48 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3WU2 Resolution: 1.15→26.454 Å / SU ML: 0.09 / σ(F): 1.36 / Phase error: 17.69 / 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: 26.15 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→26.454 Å
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Refine LS restraints |
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LS refinement shell |
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