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- PDB-1c3w: BACTERIORHODOPSIN/LIPID COMPLEX AT 1.55 A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1c3w
TitleBACTERIORHODOPSIN/LIPID COMPLEX AT 1.55 A RESOLUTION
ComponentsBACTERIORHODOPSIN (GROUND STATE WILD TYPE "BR")
KeywordsION TRANSPORT / ION PUMP / MEMBRANE PROTEIN / RETINAL PROTEIN / LIPIDS / PHOTORECEPTOR / HALOARCHAEA / 7-TRANSMEMBRANE / SERPENTINE / MEROHEDRAL TWINNING
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
Chem-LI1 / RETINAL / 2,10,23-TRIMETHYL-TETRACOSANE / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 Å
AuthorsLuecke, H.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Structure of bacteriorhodopsin at 1.55 A resolution.
Authors: Luecke, H. / Schobert, B. / Richter, H.T. / Cartailler, J.P. / Lanyi, J.K.
#1: Journal: Science / Year: 1998
Title: Proton Transfer Pathways in Bacteriorhodopsin at 2.3 Angstrom Resolution
Authors: Luecke, H. / Richter, H.-T. / Lanyi, J.K.
History
DepositionJul 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BACTERIORHODOPSIN (GROUND STATE WILD TYPE "BR")
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,31816
Polymers24,3441
Non-polymers8,97415
Water41423
1
A: BACTERIORHODOPSIN (GROUND STATE WILD TYPE "BR")
hetero molecules

A: BACTERIORHODOPSIN (GROUND STATE WILD TYPE "BR")
hetero molecules

A: BACTERIORHODOPSIN (GROUND STATE WILD TYPE "BR")
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,95348
Polymers73,0323
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 area27150 Å2
ΔGint-231 kcal/mol
Surface area27390 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.631, 60.631, 108.156
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Detailshomotrimer constructed from symmetry-related monomers

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Components

#1: Protein BACTERIORHODOPSIN (GROUND STATE WILD TYPE "BR")


Mass: 24343.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SCHIFF BASE LINKAGE BETWEEN LYS 216 (NZ) AND RET 301 (C15) DIETHER LIPID BILAYER
Source: (gene. exp.) Halobacterium salinarum (Halophile) / Description: THIS SEQUENCE OCCURS NATURALLY IN H. SALINARUM / Cellular location: PLASMA MEMBRANE / Cellular location (production host): CYTOPLASM / Production host: Halobacterium salinarum (Halophile) / References: UniProt: P02945
#2: 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
#3: Chemical ChemComp-SQU / 2,10,23-TRIMETHYL-TETRACOSANE / LIPID FRAGMENT


Mass: 380.734 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H56
#4: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#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: 2.65 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 293 K / Method: cubic lipid phase / pH: 5.6
Details: MO:WATER:PHOSPHATE, pH 5.6, CUBIC LIPID PHASE, temperature 20K
Crystal
*PLUS
Crystal grow
*PLUS
Method: cubic lipid phase
Details: Landau, E.M., (1996) Proc.Natl.Acad.Sci.USA., 93, 14532.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.3 Msodium potassium Pi11
23.5 mg/mlprotein11
30.05 %methylpentandiol11
41.2 %beta-octylglycopyranoside11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC / Detector: CCD / Date: Jul 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→25 Å / Num. all: 372549 / Num. obs: 34002 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.069 / Net I/σ(I): 19.9
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 2 / % possible all: 97.2
Reflection
*PLUS
Num. measured all: 372549

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementStarting model: PDB ENTRY 1BRX

1brx


Resolution: 1.55→12 Å / Num. parameters: 8300 / Num. restraintsaints: 8209 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: MEROHEDRAL TWINNING RATIO OF 76:24
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1687 5 %THIN RESOLUTION SHELLS
obs0.158 -99.1 %-
all-32249 --
Solvent computationSolvent model: SHELXL-97 SWAT, BABINET'S PRINCIPLE
Refine analyzeNum. disordered residues: 0 / Occupancy sum non hydrogen: 2073
Refinement stepCycle: LAST / Resolution: 1.55→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1720 0 330 23 2073
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.264
X-RAY DIFFRACTIONs_zero_chiral_vol0.072
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.079
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.013
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rwork: 0.158
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.03

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