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- PDB-1c8s: BACTERIORHODOPSIN D96N LATE M STATE INTERMEDIATE -

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Basic information

Entry
Database: PDB / ID: 1c8s
TitleBACTERIORHODOPSIN D96N LATE M STATE INTERMEDIATE
ComponentsBACTERIORHODOPSIN ("M" STATE INTERMEDIATE)
KeywordsION TRANSPORT / ION PUMP / MEMBRANE PROTEIN / RETINAL PROTEIN / LIPIDS / PHOTORECEPTOR / HALOARCHAEA / D96N M INTERMEDIATE / MEROHEDRAL TWINNING
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 / ISOMORPHOUS / Resolution: 2 Å
AuthorsLuecke, H.
Citation
Journal: Science / Year: 1999
Title: Structural changes in bacteriorhodopsin during ion transport at 2 angstrom resolution.
Authors: Luecke, H. / Schobert, B. / Richter, H.T. / Cartailler, J.P. / Lanyi, J.K.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Structure of Bacteriorhodopsin at 1.55 Angstrom Resolution
Authors: Luecke, H. / Schobert, B. / Richter, H.-T. / Cartailler, J.-P. / Lanyi, J.K.
#2: 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 29, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 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
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 ("M" STATE INTERMEDIATE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,06514
Polymers21,3691
Non-polymers7,69613
Water25214
1
A: BACTERIORHODOPSIN ("M" STATE INTERMEDIATE)
hetero molecules

A: BACTERIORHODOPSIN ("M" STATE INTERMEDIATE)
hetero molecules

A: BACTERIORHODOPSIN ("M" STATE INTERMEDIATE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,19542
Polymers64,1083
Non-polymers23,08739
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 area26710 Å2
ΔGint-233 kcal/mol
Surface area25350 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 ("M" STATE INTERMEDIATE)


Mass: 21369.309 Da / Num. of mol.: 1 / Mutation: D96N
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) / 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.: 11 / 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.: 14 / 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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 296 K / Method: cubic lipid phase / pH: 5.6
Details: MO:WATER:PHOSPHATE, pH 5.6, CUBIC LIPID PHASE, temperature 296K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: other / Details: Gabriele, R., (1998) J. Struct. Biol., 121, 82.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.3 mg/mlprotein11
21 Msodium potassium Pi11
32.5 %MPD11

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONALS 5.0.211
SYNCHROTRONESRF ID1321
Detector
TypeIDDetector
ADSC1CCD
MAR CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 14622 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 19.2
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.1 / % possible all: 98.1
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 25 Å / Num. measured all: 110517
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 98.1 % / Rmerge(I) obs: 0.33

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: ISOMORPHOUS
Starting model: PDB ENTRY 1C3W

1c3w


Resolution: 2→12 Å / Num. parameters: 7288 / Num. restraintsaints: 7357 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: MEROHEDRAL TWINNING RATIO OF 53:47
RfactorNum. reflection% reflectionSelection details
Rfree0.219 734 5 %THIN RESOLUTION SHELLS
all0.173 14622 --
obs0.172 -95 %-
Solvent computationSolvent model: SHELXL-97 SWAT, BABINET'S PRINCIPLE
Refine analyzeNum. disordered residues: 0
Refinement stepCycle: LAST / Resolution: 2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1510 0 297 14 1821
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.261
X-RAY DIFFRACTIONs_zero_chiral_vol0.031
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.032
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.016
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: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS

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