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- PDB-1f4z: BACTERIORHODOPSIN-M PHOTOINTERMEDIATE STATE OF THE E204Q MUTANT A... -

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Basic information

Entry
Database: PDB / ID: 1f4z
TitleBACTERIORHODOPSIN-M PHOTOINTERMEDIATE STATE OF THE E204Q MUTANT AT 1.8 ANGSTROM RESOLUTION
ComponentsBACTERIORHODOPSIN
KeywordsPROTON TRANSPORT / MEMBRANE PROTEIN / ION PUMP / RETINAL PROTEIN / LIPIDS / PHOTORECEPTOR / HALOARCHAEA / 7-TRANSMEMBRANE / ION TRANSPORT / MEROHEDRAL TWINNING / E204Q mutant M state / photocycle intermediate
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
Chem-LI1 / RETINAL / 2,10,23-TRIMETHYL-TETRACOSANE / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsLuecke, H. / Schobert, B. / Cartailler, J.P. / Richter, H.T. / Rosengarth, A. / Needleman, R. / Lanyi, J.K.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Coupling photoisomerization of retinal to directional transport in bacteriorhodopsin.
Authors: Luecke, H. / Schobert, B. / Cartailler, J.P. / Richter, H.T. / Rosengarth, A. / Needleman, R. / Lanyi, J.K.
History
DepositionJun 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 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 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)33,83416
Polymers24,8601
Non-polymers8,97415
Water45025
1
A: BACTERIORHODOPSIN
hetero molecules

A: BACTERIORHODOPSIN
hetero molecules

A: BACTERIORHODOPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,50348
Polymers74,5813
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 area24790 Å2
ΔGint-225 kcal/mol
Surface area27990 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

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Components

#1: Protein BACTERIORHODOPSIN / / BR


Mass: 24860.438 Da / Num. of mol.: 1 / Mutation: E204Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium salinarum (Halophile) / 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 / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 295 K / Method: cubic lipid phase / pH: 5.6
Details: MO:WATER:PHOSPHATE, pH 5.6, Cubic lipid phase, temperature 295K
Crystal grow
*PLUS
Temperature: 20 ℃
Details: Landau, E.M., (1996) Proc.Natl.Acad.Sci.USA., 93, 14532.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
160-70 %(w/v)lipids11
22.5-4.5 mg/mlBR11
30.7-4.0 Msodium potassium phosphate11
41.5-3.75 %MPD11
50.36-0.48 %OG11

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSSRL BL9-211
SYNCHROTRONESRF ID1321
SYNCHROTRONSPring-8 BL41XU31
Detector
TypeIDDetectorDate
ADSC QUANTUM1CCDJan 5, 2000
MAR-CCD2CCDFeb 17, 2000
MAR-CCD3CCDMar 27, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 214773 / Num. obs: 21451 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 28.2
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 3.3 / % possible all: 95.1
Reflection
*PLUS
Num. measured all: 214773
Reflection shell
*PLUS
% possible obs: 95.1 %

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementStarting model: ISOMORPHOUS WITH 1C3W

1c3w


Resolution: 1.8→12 Å / Num. parameters: 8252 / Num. restraintsaints: 8198 / Cross valid method: 5% / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Twin ratio is 58:42, R-factor (F>4sig)=0.131, R-free (F>4sig)=0.190
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1039 -5% of the data was omitted via thin-resolution shell selection
Rwork0.142 ---
all-20778 --
obs-20778 99.5 %-
Refinement stepCycle: LAST / Resolution: 1.8→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1720 0 330 25 2075
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.024
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 12 Å / σ(F): 4 / % reflection Rfree: 5 % / Rfactor all: 0.142 / Rfactor obs: 0.131
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.024

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