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- PDB-3utv: Crystal structure of bacteriorhodopsin mutant Y57F -

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Basic information

Entry
Database: PDB / ID: 3utv
TitleCrystal structure of bacteriorhodopsin mutant Y57F
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / MEMBRANE PROTEIN / PHOTORECEPTOR PROTEIN / RETINAL PROTEIN / ION TRANSPORT / SENSORY TRANSDUCTION
Function / homology
Function and homology information


light-driven active monoatomic ion transmembrane transporter activity / photoreceptor activity / phototransduction / monoatomic ion channel activity / proton transmembrane transport / 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
1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium sp. (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsCao, Z. / Bowie, J.U.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Shifting hydrogen bonds may produce flexible transmembrane helices.
Authors: Cao, Z. / Bowie, J.U.
History
DepositionNov 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8763
Polymers26,9141
Non-polymers9622
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7526
Polymers53,8272
Non-polymers1,9254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5670 Å2
ΔGint-43 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.080, 104.009, 129.743
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Bacteriorhodopsin / BR / Bacterioopsin / BO


Mass: 26913.500 Da / Num. of mol.: 1 / Mutation: Y57F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium sp. (Halophile) / Strain: ATCC 700922 / JCM 11081 / NRC-1 / Gene: bop, VNG_1467G / Production host: Halobacterium salinarum (Halophile) / Strain (production host): L33 / References: UniProt: P02945
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-MC3 / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE


Mass: 677.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H72NO8P / Comment: phospholipid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.89 Å3/Da / Density % sol: 57.41 %
Crystal growTemperature: 310 K / Method: bicelles, vapor diffusion, hanging drop / pH: 4
Details: 0.65M sodium phosphate, 0.95% triethylene glycerol, 0.008M 1,6-hexanediol, 4.3% DMPC, 1.5% CHAPSO, BICELLES, VAPOR DIFFUSION, HANGING DROP, temperature 310K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97938 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 26, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97938 Å / Relative weight: 1
ReflectionResolution: 2.06→100 Å / Num. all: 19418 / Num. obs: 19418 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.06→2.13 Å / % possible all: 97.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→40.07 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.648 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21044 1560 8 %RANDOM
Rwork0.19588 ---
obs0.19707 17856 98.49 %-
all-17856 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.603 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.61 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.06→40.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 66 10 1831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221868
X-RAY DIFFRACTIONr_bond_other_d0.0010.021246
X-RAY DIFFRACTIONr_angle_refined_deg1.9522.0032542
X-RAY DIFFRACTIONr_angle_other_deg1.25433038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4035226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.31222.06958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98615284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.695157
X-RAY DIFFRACTIONr_chiral_restr0.2240.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211994
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02409
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_it2.1591.51124
X-RAY DIFFRACTIONr_mcbond_other0.8231.5467
X-RAY DIFFRACTIONr_mcangle_it3.19521802
X-RAY DIFFRACTIONr_scbond_it4.8643744
X-RAY DIFFRACTIONr_scangle_it7.1674.5740
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.06→2.115 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 109 -
Rwork0.195 1249 -
obs--93.21 %
Refinement TLS params.Method: refined / Origin x: -21.5147 Å / Origin y: -15.0865 Å / Origin z: 3.2416 Å
111213212223313233
T0.0531 Å20.0099 Å20.0041 Å2-0.0203 Å2-0.0052 Å2--0.0323 Å2
L0.8209 °2-0.1918 °20.1319 °2-0.9531 °20.0346 °2--0.3233 °2
S0.0189 Å °0.0874 Å °-0.0447 Å °-0.1147 Å °-0.0221 Å °0.0112 Å °0.08 Å °0.0659 Å °0.0032 Å °

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