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- PDB-3uty: Crystal structure of bacteriorhodopsin mutant P50A/T46A -

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Basic information

Entry
Database: PDB / ID: 3uty
TitleCrystal structure of bacteriorhodopsin mutant P50A/T46A
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 / monoatomic ion channel activity / photoreceptor activity / phototransduction / 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
DODECANE / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium sp. (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 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 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriorhodopsin
B: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4865
Polymers53,7472
Non-polymers7393
Water1267
1
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3283
Polymers26,8731
Non-polymers4552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1582
Polymers26,8731
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-21 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.781, 116.463, 57.083
Angle α, β, γ (deg.)90.00, 112.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bacteriorhodopsin / BR / Bacterioopsin / BO


Mass: 26873.436 Da / Num. of mol.: 2 / Mutation: P50A, T46A
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.: 2 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.61 Å3/Da / Density % sol: 52.96 %
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: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 7, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.37→90 Å / Num. all: 21876 / Num. obs: 21876 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.37→2.45 Å / % possible all: 96.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
CNS1.3refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→90 Å / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflectionSelection details
Rfree0.2388 1111 RANDOM
Rwork0.2142 --
all0.2154 22454 -
obs0.2154 21088 -
Displacement parametersBiso mean: 36.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.37 Å20 Å2-2.517 Å2
2--11.933 Å20 Å2
3----9.563 Å2
Refinement stepCycle: LAST / Resolution: 2.37→90 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3504 0 52 7 3563
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg2.016

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