+Open data
-Basic information
Entry | Database: PDB / ID: 1brr | ||||||||||||
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Title | X-RAY STRUCTURE OF THE BACTERIORHODOPSIN TRIMER/LIPID COMPLEX | ||||||||||||
Components | PROTEIN (BACTERIORHODOPSIN) | ||||||||||||
Keywords | PROTON TRANSPORT / PROTON PUMP / MEMBRANE PROTEIN / RETINAL PROTEIN / LIPIDS / PHOTORECEPTOR / HALOARCHAEA | ||||||||||||
Function / homology | Function and homology information light-driven active monoatomic ion transmembrane transporter activity / photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Halobacterium salinarum (Halophile) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||||||||
Authors | Essen, L.-O. / Siegert, R. / Oesterhelt, D. | ||||||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 Title: Lipid patches in membrane protein oligomers: crystal structure of the bacteriorhodopsin-lipid complex Authors: Essen, L. / Siegert, R. / Lehmann, W.D. / Oesterhelt, D. #1: Journal: J.Mol.Biol. / Year: 1993 Title: Orthorhombic Crystal Form of Bacteriorhodopsin Nucleated on Benzamidine Diffracting to 3.6 Angstrom Resolution Authors: Schertler, G.F.X. / Bartunik, H.D. / Michel, H. / Oesterhelt, D. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1brr.cif.gz | 152.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1brr.ent.gz | 119.9 KB | Display | PDB format |
PDBx/mmJSON format | 1brr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1brr_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 1brr_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 1brr_validation.xml.gz | 31.6 KB | Display | |
Data in CIF | 1brr_validation.cif.gz | 40.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/1brr ftp://data.pdbj.org/pub/pdb/validation_reports/br/1brr | HTTPS FTP |
-Related structure data
Related structure data | 2brdS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper:
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 26740.330 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: SCHIFF BASE BETWEEN LYS 216 AND RET 999 / Source: (natural) Halobacterium salinarum (Halophile) / Cellular location: MEMBRANE / Strain: R1 / References: UniProt: P02945 |
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-Sugars , 2 types, 3 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-BGC / | |
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-Non-polymers , 4 types, 17 molecules
#3: Chemical | #4: Chemical | ChemComp-ARC / #5: Chemical | #7: Chemical | ChemComp-OCT / | |
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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: 3.18 Å3/Da / Density % sol: 54 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.2 / Details: SEE REFERENCE 2, pH 5.2 | |||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion / PH range low: 5.6 / PH range high: 5.4 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1997 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→25 Å / Num. obs: 18504 / % possible obs: 82.3 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.9→3.03 Å / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 5.7 / % possible all: 43.6 |
Reflection | *PLUS Num. measured all: 48145 |
Reflection shell | *PLUS % possible obs: 43.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BRD Resolution: 2.9→10 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 58.2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→10 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 2.9→3.03 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 3 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 58.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.9 Å / Rfactor Rfree: 0.297 / % reflection Rfree: 3 % / Rfactor Rwork: 0.214 |