+Open data
-Basic information
Entry | Database: PDB / ID: 1z9k | ||||||
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Title | Photosynthetic Reaction Center from Rhodobacter sphaeroides | ||||||
Components | (Reaction center protein ...Photosynthetic reaction centre) x 3 | ||||||
Keywords | PHOTOSYNTHESIS / ALPHA HELIX / MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information : / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / membrane => GO:0016020 / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodobacter sphaeroides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 4.6 Å | ||||||
Authors | Camara-Artigas, A. / 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: Uyeda, G. / Camara-Artigas, A. / Williams, J.C. / Allen, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z9k.cif.gz | 171.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z9k.ent.gz | 128 KB | Display | PDB format |
PDBx/mmJSON format | 1z9k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/1z9k ftp://data.pdbj.org/pub/pdb/validation_reports/z9/1z9k | HTTPS FTP |
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-Related structure data
Related structure data | 1z9jC 1m3xS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Reaction center protein ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 31346.389 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: pufL / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P02954, UniProt: P0C0Y8*PLUS |
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#2: Protein | Mass: 34398.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: pufM / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P02953, UniProt: P0C0Y9*PLUS |
#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) / References: UniProt: P11846, UniProt: P0C0Y7*PLUS |
-Non-polymers , 5 types, 10 molecules
#4: Chemical | ChemComp-BCL / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-FE / | #8: Chemical | ChemComp-MN / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.3 Å3/Da / Density % sol: 80 % |
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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 |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 20, 2003 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 4.6→25 Å / Num. all: 32336 / Num. obs: 12646 / % possible obs: 94.15 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 120 Å2 / Rmerge(I) obs: 0.182 / Rsym value: 0.22 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 4.6→4.85 Å / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1m3x Resolution: 4.6→25 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Babinet bulk solvent scaling
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Displacement parameters | Biso mean: 90 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 4.6→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.5→4.78 Å / Rfactor Rfree error: 0.036
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Xplor file |
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