+Open data
-Basic information
Entry | Database: PDB / ID: 1z9j | ||||||
---|---|---|---|---|---|---|---|
Title | Photosynthetic Reaction Center from Rhodobacter sphaeroides | ||||||
Components | (Reaction center protein ...Photosynthetic reaction centre) x 3 | ||||||
Keywords | PHOTOSYNTHESIS / Alpha Helix / Membrane Protein / Mutant | ||||||
Function / homology | Function and homology information plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodobacter sphaeroides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 4.5 Å | ||||||
Authors | Thielges, M. / Uyeda, G. / Camara-Artigas, A. / Kalman, L. / Williams, J.C. / Allen, J.P. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Design of a Redox-Linked Active Metal Site: Manganese Bound to Bacterial Reaction Centers at a Site Resembling That of Photosystem II Authors: Thielges, M. / Uyeda, G. / Camara-Artigas, A. / Kalman, L. / Williams, J.C. / Allen, J.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1z9j.cif.gz | 171 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1z9j.ent.gz | 128.1 KB | Display | PDB format |
PDBx/mmJSON format | 1z9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/1z9j ftp://data.pdbj.org/pub/pdb/validation_reports/z9/1z9j | HTTPS FTP |
---|
-Related structure data
Related structure data | 1z9kC 1m3xS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Reaction center protein ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 31371.377 Da / Num. of mol.: 1 / Mutation: L131H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: pufL / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): delLM1.1 / References: UniProt: P0C0Y8 |
---|---|
#2: Protein | Mass: 34476.438 Da / Num. of mol.: 1 / Mutation: L160H, R164Y, M168E, F197H, G288D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: pufM / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): delLM1.1 / References: UniProt: P0C0Y9 |
#3: Protein | Mass: 28066.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: puhA / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): delLM1.1 / References: UniProt: P0C0Y7 |
-Non-polymers , 6 types, 12 molecules
#4: Chemical | ChemComp-BCL / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-FE / | #8: Chemical | ChemComp-MN / | #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 6.3 Å3/Da / Density % sol: 80 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG,NaCl,MnCl, LDAO, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 8, 2003 / Details: graphite |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 4.5→25 Å / Num. all: 65241 / Num. obs: 13804 / % possible obs: 87.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 120 Å2 / Rmerge(I) obs: 0.19 / Rsym value: 0.17 / Net I/σ(I): 3.1 |
Reflection shell | Resolution: 4.5→4.8 Å / Rmerge(I) obs: 0.86 / % possible all: 92 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1m3x Resolution: 4.5→19.96 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 4332507.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 283.89 Å2 / ksol: 0.646587 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 90 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.5→19.96 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 4.5→4.78 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|