+Open data
-Basic information
Entry | Database: PDB / ID: 1kgb | ||||||
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Title | structure of ground-state bacteriorhodopsin | ||||||
Components | bacteriorhodopsin | ||||||
Keywords | PROTON TRANSPORT / bacteriorhodopsin / ground-state | ||||||
Function / homology | Function and homology information 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: 1.65 Å | ||||||
Authors | Facciotti, M.T. / Rouhani, S. / Burkard, F.T. / Betancourt, F.M. / Downing, K.H. / Rose, R.B. / McDermott, G. / Glaeser, R.M. | ||||||
Citation | Journal: Biophys.J. / Year: 2001 Title: Structure of an early intermediate in the M-state phase of the bacteriorhodopsin photocycle. Authors: Facciotti, M.T. / Rouhani, S. / Burkard, F.T. / Betancourt, F.M. / Downing, K.H. / Rose, R.B. / McDermott, G. / Glaeser, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kgb.cif.gz | 71.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kgb.ent.gz | 51.1 KB | Display | PDB format |
PDBx/mmJSON format | 1kgb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/1kgb ftp://data.pdbj.org/pub/pdb/validation_reports/kg/1kgb | HTTPS FTP |
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-Related structure data
Related structure data | 1kg8C 1kg9C 1c3wS 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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Unit cell |
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-Components
#1: Protein | Mass: 25301.916 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum (Halophile) / References: UniProt: P02945 | ||
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#2: Chemical | ChemComp-RET / | ||
#3: Chemical | ChemComp-LI1 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.86 % | ||||||||||||||||||
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Crystal grow | Method: mono-olein cubic phase / pH: 5.6 Details: 3.0M Na/K Phosphate, pH 5.6, mono-olein cubic phase, temperature 100K | ||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||
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: ALS / Beamline: 5.0.2 / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 29, 1999 |
Radiation | Monochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→20 Å / Num. all: 26695 / Num. obs: 26695 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.036 / Net I/σ(I): 32.8 |
Reflection shell | Resolution: 1.65→1.7 Å / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 3.2 / % possible all: 96.8 |
Reflection | *PLUS Lowest resolution: 20 Å / Rmerge(I) obs: 0.036 |
Reflection shell | *PLUS % possible obs: 96.8 % / Rmerge(I) obs: 0.358 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1C3W Resolution: 1.65→20 Å / σ(F): 0 / Stereochemistry target values: NULL
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Refinement step | Cycle: LAST / Resolution: 1.65→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Num. reflection obs: 25672 / σ(F): 0 / Rfactor all: 0.184 / Rfactor obs: 0.177 / Rfactor Rfree: 0.253 / Rfactor Rwork: 0.177 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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