+Open data
-Basic information
Entry | Database: PDB / ID: 5g39 | ||||||
---|---|---|---|---|---|---|---|
Title | PsbO subunit of Photosystem II, beta barrel domain at 297K, 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 stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / plasma membrane-derived thylakoid membrane Similarity search - Function | ||||||
Biological species | THERMOSYNECHOCOCCUS ELONGATUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 |
| ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5g39.cif.gz | 82.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5g39.ent.gz | 63.1 KB | Display | PDB format |
PDBx/mmJSON format | 5g39.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/5g39 ftp://data.pdbj.org/pub/pdb/validation_reports/g3/5g39 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5g38C 5g3aC 3wu2S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-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 |
---|---|
#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: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.3 % / Description: NONE |
---|---|
Crystal grow | Method: vapor diffusion / pH: 6 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: 297 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.89 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 5, 2015 / Details: MIRRORS |
Radiation | Monochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.89 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→21.13 Å / Num. obs: 29709 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 24.5 % / Biso Wilson estimate: 18.23 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 20.97 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 24.9 % / Mean I/σ(I) obs: 1.69 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3WU2 Resolution: 1.5→21.715 Å / SU ML: 0.15 / σ(F): 1.36 / Phase error: 17.45 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→21.715 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|