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- PDB-2i1x: Bacteriorhodopsin/lipid complex, D96A mutant -

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Basic information

Entry
Database: PDB / ID: 2i1x
TitleBacteriorhodopsin/lipid complex, D96A mutant
ComponentsBacteriorhodopsin
KeywordsTRANSPORT PROTEIN / ION PUMP / MEMBRANE PROTEIN / RETINAL PROTEIN / LIPIDS / PHOTORECEPTOR / HALOARCHAEA / 7-TRANSMEMBRANE / SERPENTINE / ION TRANSPORT
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
Chem-LI1 / RETINAL / 2,10,23-TRIMETHYL-TETRACOSANE / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLanyi, J.K. / Schobert, B.
CitationJournal: Biochemistry / Year: 2006
Title: Propagating Structural Perturbation Inside Bacteriorhodopsin: Crystal Structures of the M State and the D96A and T46V Mutants.
Authors: Lanyi, J.K. / Schobert, B.
History
DepositionAug 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 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 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 600SCHIFF BASE LINKAGE BETWEEN LYS 216 (NZ) AND RET 301 (C15) DIETHER LIPID BILAYER

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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)35,85916
Polymers26,8851
Non-polymers8,97415
Water41423
1
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,57848
Polymers80,6563
Non-polymers26,92245
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area23240 Å2
ΔGint-218 kcal/mol
Surface area26060 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.952, 60.952, 109.326
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Bacteriorhodopsin / BR


Mass: 26885.490 Da / Num. of mol.: 1 / Mutation: D96A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium salinarum (Halophile) / Cellular location: PLASMA MEMBRANE / Plasmid: PBA2 / Cellular location (production host): CYTOPLASM / Production host: Halobacterium salinarum (Halophile) / Strain (production host): MPK409 / 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-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.: 13 / Source method: obtained synthetically / Formula: C42H86O3
#4: Chemical ChemComp-SQU / 2,10,23-TRIMETHYL-TETRACOSANE / LIPID FRAGMENT


Mass: 380.734 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H56
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 1.8 Å3/Da / Density % sol: 47.91 %
Crystal growTemperature: 295 K / Method: cubic lipid phase / pH: 5.6
Details: MO:WATER:PHOSPHATE, pH 5.60, CUBIC LIPID PHASE, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97977 / Wavelength: 0.97977 Å
DetectorType: ADSC QUANTUM / Detector: CDD / Date: Apr 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97977 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 15618 / % possible obs: 99.99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 23.4
Reflection shellResolution: 2→2.09 Å / Rmerge(I) obs: 0.756 / Mean I/σ(I) obs: 2.9 / Num. unique all: 15618 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SHELXmodel building
SHELXL-97refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C3W

1c3w


Resolution: 2→25 Å / Num. parameters: 8284 / Num. restraintsaints: 8217 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: NO MEROHEDRAL TWINNING
RfactorNum. reflection% reflectionSelection details
Rfree0.299 745 5 %RANDOM
Rwork0.2379 ---
all0.239 15552 --
obs0.239 15618 99.9 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum non hydrogen: 2067
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1717 0 330 23 2070
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.054
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.0166
X-RAY DIFFRACTIONs_zero_chiral_vol0.022
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.026
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.046
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.074
X-RAY DIFFRACTIONs_approx_iso_adps

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