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- PDB-4hyx: Crystal Structure Analysis of the Bacteriorhodopsin in Facial Amp... -

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Basic information

Entry
Database: PDB / ID: 4hyx
TitleCrystal Structure Analysis of the Bacteriorhodopsin in Facial Amphiphile-4 DMPC Bicelle
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / Facial Amphiphile-4 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
Bacterial rhodopsins retinal binding site. / Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
TETRADECANE / DECANE / HEXANE / N-OCTANE / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsLee, S. / Stout, C.D. / Zhang, Q.
CitationJournal: 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
DepositionNov 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacteriorhodopsin
B: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,08119
Polymers56,5402
Non-polymers2,54117
Water70339
1
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4949
Polymers28,2701
Non-polymers1,2248
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,58610
Polymers28,2701
Non-polymers1,3169
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.890, 112.920, 56.290
Angle α, β, γ (deg.)90.00, 113.83, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A6 - 230
2010B6 - 230

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bacteriorhodopsin / BR / Bacterioopsin / BO


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 , 7 types, 56 molecules

#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical
ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18
#4: Chemical
ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H22
#5: Chemical ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14
#6: Chemical ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2011
RadiationMonochromator: 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 wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2→56.46 Å / Num. all: 35212 / Num. obs: 32607 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 6.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2 / % possible all: 86

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASESphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→46.85 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.009 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21388 1759 5.2 %RANDOM
Rwork0.17896 ---
obs0.18086 32391 95.66 %-
all-33860 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.358 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.99→46.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3537 0 178 39 3754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.023797
X-RAY DIFFRACTIONr_bond_other_d0.0080.023932
X-RAY DIFFRACTIONr_angle_refined_deg2.0112.0065126
X-RAY DIFFRACTIONr_angle_other_deg1.4639005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0675454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.70222.203118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.1215571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1241514
X-RAY DIFFRACTIONr_chiral_restr0.1590.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0214022
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02852
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 14105 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.994→2.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.168 102 -
Rwork0.121 1988 -
obs--80.85 %

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