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- PDB-1p8h: BACTERIORHODOPSIN M1 INTERMEDIATE PRODUCED AT ROOM TEMPERATURE -

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Basic information

Entry
Database: PDB / ID: 1p8h
TitleBACTERIORHODOPSIN M1 INTERMEDIATE PRODUCED AT ROOM TEMPERATURE
ComponentsBacteriorhodopsin
KeywordsPROTON 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: 1.52 Å
AuthorsLanyi, J.K.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystallographic Structures of the M and N Intermediates of Bacteriorhodopsin: Assembly of a Hydrogen-Bonded Chain of Water Molecules between Asp-96 and the Retinal Schiff Base
Authors: Schobert, B. / Brown, L.S. / Lanyi, J.K.
History
DepositionMay 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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_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
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 300 BIOMOLECULE 1 THIS ENTRY IS MADE UP OF TWO MODELS WHICH REPRESENT TWO CONFORMATIONS OF THE WILD- ... BIOMOLECULE 1 THIS ENTRY IS MADE UP OF TWO MODELS WHICH REPRESENT TWO CONFORMATIONS OF THE WILD-TYPE PROTEIN. MODEL 1 IS THE M1 INTERMEDIATE WITH OCCUPANCY OF 0.42 WHILE MODEL 2 IS THE NON-ILLUMINATED BACTERIORHODOPSIN (BR STATE) WITH OCCUPANCY OF 0.58.

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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)35,90316
Polymers26,9301
Non-polymers8,97415
Water45025
1
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,71048
Polymers80,7893
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 area26190 Å2
ΔGint-234 kcal/mol
Surface area27010 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.907, 60.907, 108.574
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: 26929.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium salinarum (Halophile) / Cellular location: PLASMA MEMBRANE / Gene: BOP / 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.: 25 / 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: 1.78 Å3/Da / Density % sol: 30.8 %
Crystal growTemperature: 295 K / Method: cubic lipid phase / pH: 5.6
Details: mono-olein, potassium phosphate, pH 5.60, CUBIC LIPID PHASE, temperature 295K
Crystal grow
*PLUS
pH: 5.6 / Method: unknown / 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.979 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Jun 27, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.52→25 Å / Num. all: 36506 / Num. obs: 36506 / % possible obs: 92.1 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.043 / Net I/σ(I): 41.5
Reflection shellResolution: 1.52→1.56 Å / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.7 / % possible all: 80.7
Reflection
*PLUS
Highest resolution: 1.52 Å / Lowest resolution: 25 Å / Num. measured all: 646932
Reflection shell
*PLUS
% possible obs: 80.7 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97model building
SHELXL-97refinement
SHELXL-97phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M0L

1m0l


Resolution: 1.52→25 Å / Num. parameters: 8321 / Num. restraintsaints: 19854 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2073 1839 5.3 %THIN SHELLS
obs0.1754 30220 92.1 %-
all-36491 --
Refine analyzeNum. disordered residues: 233 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2073.79
Refinement stepCycle: LAST / Resolution: 1.52→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1720 0 329 25 2074
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.047
X-RAY DIFFRACTIONs_from_restr_planes0.0229
X-RAY DIFFRACTIONs_zero_chiral_vol0.048
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.047
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.043
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor all: 0.172 / Rfactor Rfree: 0.207 / Rfactor Rwork: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.023
X-RAY DIFFRACTIONs_chiral_restr0.048
LS refinement shell
*PLUS
Highest resolution: 1.52 Å / Lowest resolution: 1.56 Å / Rfactor Rfree: 0.19 / Rfactor Rwork: 0.155

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