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Yorodumi- PDB-4hwl: Crystal Structure Analysis of the Bacteriorhodopsin in Facial Amp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hwl | ||||||
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Title | Crystal Structure Analysis of the Bacteriorhodopsin in Facial Amphiphile-7 DMPC Bicelle | ||||||
Components | Bacteriorhodopsin | ||||||
Keywords | PROTON TRANSPORT / Facial Amphiphile-7 DMPC Bicelle / Alpha helical 7 Transmembrane Protein / Photoreceptor / Proton Pump / Retinal Binding / Transmembrane | ||||||
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: 2 Å | ||||||
Authors | Lee, S. / Stout, C.D. / Zhang, Q. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Steroid-based facial amphiphiles for stabilization and crystallization of membrane proteins. Authors: Lee, S.C. / Bennett, B.C. / Hong, W.X. / Fu, Y. / Baker, K.A. / Marcoux, J. / Robinson, C.V. / Ward, A.B. / Halpert, J.R. / Stevens, R.C. / Stout, C.D. / Yeager, M.J. / Zhang, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hwl.cif.gz | 102 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hwl.ent.gz | 77 KB | Display | PDB format |
PDBx/mmJSON format | 4hwl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/4hwl ftp://data.pdbj.org/pub/pdb/validation_reports/hw/4hwl | HTTPS FTP |
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-Related structure data
Related structure data | 4hyxC 1kmeS 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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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 0 / Auth seq-ID: 5 - 231 / Label seq-ID: 18 - 244
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 28270.084 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum (Halophile) / Strain: S9 / References: UniProt: P02945 |
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-Non-polymers , 5 types, 42 molecules
#2: Chemical | #3: Chemical | ChemComp-HEX / #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: 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 | Density Matthews: 2.37 Å3/Da / Density % sol: 48.08 % |
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Crystal grow | Temperature: 300.15 K / Method: vapor diffusion, sitting drop / pH: 3.4 Details: 3.6M Sodium Phosphate (pH 3.4), 3.5% Triethyleneglycol, 180mM Hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 300.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2011 |
Radiation | Monochromator: Slide scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 2→46.67 Å / Num. all: 35395 / Num. obs: 34192 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.7 / Num. unique all: 5132 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KME Resolution: 2→42.08 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.12 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.373 Å2
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Refinement step | Cycle: LAST / Resolution: 2→42.08 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 14311 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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