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- PDB-3utw: Crystal structure of bacteriorhodopsin mutant P50A/Y57F -

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Basic information

Entry
Database: PDB / ID: 3utw
TitleCrystal structure of bacteriorhodopsin mutant P50A/Y57F
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / MEMBRANE PROTEIN / PHOTORECEPTOR PROTEIN / RETINAL PROTEIN / ION TRANSPORT / SENSORY TRANSDUCTION
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
1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium sp. (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1424
Polymers26,8871
Non-polymers1,2553
Water1629
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)56,2848
Polymers53,7752
Non-polymers2,5096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4250 Å2
ΔGint-35 kcal/mol
Surface area21410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.281, 103.059, 128.879
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: 26887.463 Da / Num. of mol.: 1 / Mutation: P50A, 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: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.8 Å3/Da / Density % sol: 56.01 %
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: 0.97916 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. all: 11638 / Num. obs: 11638 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.49 Å / % possible all: 98.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→47.85 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.912 / SU B: 14.055 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.38 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24575 929 8 %RANDOM
Rwork0.203 ---
obs0.20644 10704 95.65 %-
all-10704 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.269 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2---0.65 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1753 0 86 9 1848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.021886
X-RAY DIFFRACTIONr_bond_other_d0.0080.021263
X-RAY DIFFRACTIONr_angle_refined_deg2.4892.0112562
X-RAY DIFFRACTIONr_angle_other_deg1.32233081
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6085226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54822.06958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.42515284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.969157
X-RAY DIFFRACTIONr_chiral_restr0.2550.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021995
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02418
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_it2.5541.51123
X-RAY DIFFRACTIONr_mcbond_other0.9031.5468
X-RAY DIFFRACTIONr_mcangle_it3.80521798
X-RAY DIFFRACTIONr_scbond_it6.9353764
X-RAY DIFFRACTIONr_scangle_it8.9554.5764
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.466 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 58 -
Rwork0.206 696 -
obs--91.95 %
Refinement TLS params.Method: refined / Origin x: -21.2704 Å / Origin y: -14.8971 Å / Origin z: 3.1538 Å
111213212223313233
T0.0406 Å20.0131 Å2-0.0016 Å2-0.0164 Å2-0.004 Å2--0.0602 Å2
L0.8196 °2-0.0647 °2-0.021 °2-0.8953 °2-0.0068 °2--0.4764 °2
S0.0003 Å °0.0771 Å °-0.0344 Å °-0.1329 Å °-0.0211 Å °-0.0047 Å °0.0813 Å °0.0623 Å °0.0208 Å °

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