+Open data
-Basic information
Entry | Database: PDB / ID: 1m3x | ||||||
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Title | Photosynthetic Reaction Center From Rhodobacter Sphaeroides | ||||||
Components | (Photosynthetic Reaction center protein ...) 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Camara-Artigas, A. / Brune, D. / Allen, J.P. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: Interactions between lipids and bacterial reaction centers determined by protein crystallography. Authors: Camara-Artigas, A. / Brune, D. / Allen, J.P. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Individual interactions influence the crystalline order for membrane proteins Authors: Camara-Artigas, A. / Magee, C.L. / Williams, J.C. / Allen, J.P. | ||||||
History |
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Remark 600 | HETEROGEN THE FOLLOWING LIGANDS HAVE ATOMS MISSING DUE TO LACK OF ELECTRON DENSITY: BCL 850, U10 ...HETEROGEN THE FOLLOWING LIGANDS HAVE ATOMS MISSING DUE TO LACK OF ELECTRON DENSITY: BCL 850, U10 857, U10 858, CDL 900, PC2 901, GGD 902. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m3x.cif.gz | 206.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m3x.ent.gz | 156.8 KB | Display | PDB format |
PDBx/mmJSON format | 1m3x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m3x_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
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Full document | 1m3x_full_validation.pdf.gz | 3.6 MB | Display | |
Data in XML | 1m3x_validation.xml.gz | 43.9 KB | Display | |
Data in CIF | 1m3x_validation.cif.gz | 56.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/1m3x ftp://data.pdbj.org/pub/pdb/validation_reports/m3/1m3x | HTTPS FTP |
-Related structure data
Related structure data | 1qovS 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
-Photosynthetic Reaction center protein ... , 3 types, 3 molecules LMH
#1: Protein | Mass: 31346.389 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / 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) / 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) / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P11846, UniProt: P0C0Y7*PLUS |
-Non-polymers , 10 types, 217 molecules
#4: Chemical | ChemComp-BCL / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-PC1 / | #8: Chemical | ChemComp-FE / | #9: Chemical | ChemComp-CL / | #10: Chemical | ChemComp-SPO / | #11: Chemical | ChemComp-CDL / | #12: Chemical | ChemComp-GGD / | #13: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: POTASIUM PHOSPHATE, LDAO, HEPTANE TRIOL, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2000 Details: 58 cm long, Pt-coated, fused silica, vertical focus mirror; Cyclindrically bent triangular Si(111) asymmetric cut |
Radiation | Monochromator: horizontal focus monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→30.83 Å / Num. obs: 68970 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.126 / Rsym value: 0.109 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 2.55→2.69 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 1.5 / Num. unique all: 34173 / Rsym value: 0.364 / % possible all: 92.5 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 69691 / Num. measured all: 564825 |
Reflection shell | *PLUS Lowest resolution: 2.65 Å / % possible obs: 92.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1QOV Resolution: 2.55→29.91 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.9782 Å2 / ksol: 0.326599 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.3 Å2
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Refine analyze | Luzzati coordinate error free: 0.29 Å / Luzzati sigma a free: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→29.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.71 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å / Rfactor Rfree: 0.205 / Rfactor Rwork: 0.183 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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