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- PDB-1s54: Thr24Ala Bacteriorhodopsin -

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Basic information

Entry
Database: PDB / ID: 1s54
TitleThr24Ala Bacteriorhodopsin
Componentsbacteriorhodopsin
KeywordsPROTON TRANSPORT / membrane protein / bacteriorhodopsin / bicelle
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
RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYohannan, S. / Faham, S. / Yang, D. / Grosfeld, D. / Chamberlain, A.K. / Bowie, J.U.
CitationJournal: J.Am.Chem.Soc. / Year: 2004
Title: A C(alpha)-H.O Hydrogen Bond in a Membrane Protein Is Not Stabilizing
Authors: Yohannan, S. / Faham, S. / Yang, D. / Grosfeld, D. / Chamberlain, A.K. / Bowie, J.U.
History
DepositionJan 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 1.4Aug 23, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: bacteriorhodopsin
B: bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2324
Polymers49,6632
Non-polymers5692
Water1,35175
1
A: bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1162
Polymers24,8311
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1162
Polymers24,8311
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.182, 108.366, 55.685
Angle α, β, γ (deg.)90.00, 113.68, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein bacteriorhodopsin / BR


Mass: 24831.396 Da / Num. of mol.: 2 / Mutation: T24A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium salinarum (Halophile)
Description: DNA transformed into E. coli, then transformed into Halobacterium Salinarum where the protein is expressed.
Production host: Halobacterium salinarum (Halophile) / Strain (production host): L33 / References: UniProt: P02945
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.46 Å3/Da / Density % sol: 49.94 %
Crystal growTemperature: 310 K / Method: bicelle hanging drop vapor diffusion / pH: 3.7
Details: Sodium Phosphate, Hexanediol, pH 3.7, bicelle hanging drop vapor diffusion, temperature 310K
Crystal grow
*PLUS
Temperature: 37 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.5 M1reservoirpH3.7NaH2PO4
20.060 Mhexanediol1reservoir
340 %(w/v)protein/bicelle solution1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 23072 / Num. obs: 23072 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 0.131 / Net I/σ(I): 8.34
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 3.6 / Num. unique all: 2214 / % possible all: 91.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PY6

1py6


Resolution: 2.2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Crystal twinning was observed. Twinning operation = -h, -k, h+l. Twinning Fraction = 0.5
RfactorNum. reflection% reflectionSelection details
Rfree0.2873 1245 5.5 %SHELLS
Rwork0.2433 ---
all0.24551 22608 --
obs0.24551 22608 92.8 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.095 Å20 Å23.83 Å2
2---13.065 Å20 Å2
3---5.97 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3510 0 40 75 3625
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.097
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_dihedral_angle_d18.1
X-RAY DIFFRACTIONc_improper_angle_d0.758
X-RAY DIFFRACTIONc_mcbond_it1.1661.5
X-RAY DIFFRACTIONc_scbond_it1.5962
X-RAY DIFFRACTIONc_mcangle_it1.8532
X-RAY DIFFRACTIONc_scangle_it2.2672.5
Refinement
*PLUS
Highest resolution: 2.2 Å / Rfactor Rfree: 0.287 / Rfactor Rwork: 0.243
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.758

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