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- PDB-1m0m: BACTERIORHODOPSIN M1 INTERMEDIATE AT 1.43 A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1m0m
TitleBACTERIORHODOPSIN M1 INTERMEDIATE AT 1.43 A RESOLUTION
ComponentsBACTERIORHODOPSIN
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 / 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: 1.43 Å
AuthorsLanyi, J.K.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Crystallographic structure of the retinal and the protein after deprotonation of the Schiff base: the switch in the bacteriorhodopsin photocycle.
Authors: Lanyi, J. / Schobert, B.
History
DepositionJun 13, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 9, 2015Group: Version format compliance
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE 1 THIS ENTRY IS MADE UP OF TWO MODELS WHICH REPRESENT THE TWO CONFORMATIONS OF THE WILD- ...BIOMOLECULE 1 THIS ENTRY IS MADE UP OF TWO MODELS WHICH REPRESENT THE TWO CONFORMATIONS OF THE WILD-TYPE PROTEIN. MODEL 1 IS THE BR STATE WITH OCCUPANCY OF 0.40 AND MODEL 2 IS THE MI STATE WITH OCCUPANCY OF 0.60.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BACTERIORHODOPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,24416
Polymers28,2701
Non-polymers8,97415
Water41423
1
A: BACTERIORHODOPSIN
hetero molecules

A: BACTERIORHODOPSIN
hetero molecules

A: BACTERIORHODOPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,73248
Polymers84,8103
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
Unit cell
Length a, b, c (Å)61.069, 61.069, 110.099
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Number of models2

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Components

#1: Protein BACTERIORHODOPSIN / BR


Mass: 28270.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium salinarum (Halophile) / Cellular location: PLASMA MEMBRANE / Plasmid: PRN2367 / Cellular location (production host): CYTOPLASM / Production host: Halobacterium salinarum (Halophile) / 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: 1.81 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 295 K / Method: cubic lipid phase / pH: 5.6
Details: cubic lipid phase with mono-olein and potassium phosphate, pH 5.60, CUBIC LIPID PHASE, temperature 295K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.6
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: 0.979 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Aug 20, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.43→25 Å / Num. obs: 39522 / % possible obs: 92.2 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.05 / Net I/σ(I): 39.6
Reflection shellResolution: 1.43→1.47 Å / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 3.5 / % possible all: 96.6
Reflection
*PLUS
Highest resolution: 1.43 Å / Lowest resolution: 25 Å / Num. measured all: 517904 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 96.6 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 3.5

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C3W

1c3w


Resolution: 1.43→25 Å / Num. parameters: 8453 / Num. restraintsaints: 8759 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: MEROHEDRAL TWINNING RATIO OF 52:48
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1907 4.8 %THIN RESOLUTION SHELLS
Rwork0.163 ---
all0.1644 39496 --
obs0.1631 39496 92.2 %-
Refine analyzeNum. disordered residues: 21 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2070.9
Refinement stepCycle: LAST / Resolution: 1.43→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1720 0 330 23 2073
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0244
X-RAY DIFFRACTIONs_zero_chiral_vol0.173
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.052
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.009
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor all: 0.1644 / Rfactor obs: 0.1631 / Rfactor Rfree: 0.213 / Rfactor Rwork: 0.163
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.43 Å / Lowest resolution: 1.47 Å / Rfactor Rfree: 0.198 / Rfactor Rwork: 0.142

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