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- PDB-1mgy: Structure of the D85S mutant of bacteriorhodopsin with bromide bound -

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Basic information

Entry
Database: PDB / ID: 1mgy
TitleStructure of the D85S mutant of bacteriorhodopsin with bromide bound
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / bacteriorhodopsin / anion / pump / bromide / halide
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
BROMIDE ION / : / Chem-LI1 / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFacciotti, M.T. / Cheung, V.S. / Nguyen, D. / Rouhani, S. / Glaeser, R.M.
CitationJournal: Biophys.J. / Year: 2003
Title: Crystal Structure of the Bromide-Bound D85S Mutant of Bacteriorhodopsin: Principles of Ion Pumping
Authors: Facciotti, M.T. / Cheung, V.S. / Nguyen, D. / Rouhani, S. / Glaeser, R.M.
History
DepositionAug 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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
Revision 1.4Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature

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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)32,49813
Polymers26,9011
Non-polymers5,59612
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.498, 121.326, 73.875
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bacteriorhodopsin / BR


Mass: 26901.490 Da / Num. of mol.: 1 / Mutation: D85S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium salinarum (Halophile) / Production host: Halobacterium salinarum (Halophile) / References: UniProt: P02945

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Non-polymers , 5 types, 59 molecules

#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#5: Chemical
ChemComp-LI1 / 1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL / LIPID FRAGMENT


Mass: 639.130 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C42H86O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.72 %
Crystal growTemperature: 293 K / Method: connected bilayer gel / pH: 4.6
Details: Sodium Acetate, PEG 4000, potassium chloride, mono-olein, pH 4.6, connected bilayer gel, temperature 293K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein11
2100 mMsodium acetate12pH4.6
3200 mM12KCl
410 %PEG400012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1272 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 7, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionResolution: 2→60 Å / Num. all: 16336 / Num. obs: 16336 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.07 Å / % possible all: 89.8
Reflection
*PLUS
Highest resolution: 2 Å / Num. measured all: 135550 / Rmerge(I) obs: 0.127
Reflection shell
*PLUS
% possible obs: 89.8 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1KGB

1kgb


Resolution: 2→12 Å / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.236 777 random
Rwork0.215 --
all-15316 -
obs-15316 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.799 Å20 Å20 Å2
2---1.175 Å20 Å2
3---0.375 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1689 0 81 49 1819
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_d0.953
X-RAY DIFFRACTIONc_bond_d0.006859
X-RAY DIFFRACTIONc_dihedral_angle_d18.05
X-RAY DIFFRACTIONc_improper_angle_d1.023
X-RAY DIFFRACTIONc_mcbond_it1.3791.5
X-RAY DIFFRACTIONc_scbond_it2.0942
X-RAY DIFFRACTIONc_mcangle_it2.1442
X-RAY DIFFRACTIONc_scangle_it3.0182.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein.param2
X-RAY DIFFRACTION2ret.par
X-RAY DIFFRACTION3water.param
X-RAY DIFFRACTION4li1.par
X-RAY DIFFRACTION5ion.param
Refinement
*PLUS
Lowest resolution: 12 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.2365 / Rfactor Rwork: 0.2151
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg0.953
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.05
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.023

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