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- PDB-1cwq: M INTERMEDIATE STRUCTURE OF THE WILD TYPE BACTERIORHODOPSIN IN CO... -

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Basic information

Entry
Database: PDB / ID: 1cwq
TitleM INTERMEDIATE STRUCTURE OF THE WILD TYPE BACTERIORHODOPSIN IN COMBINATION WITH THE GROUND STATE STRUCTURE
ComponentsBACTERIORHODOPSIN ("M" STATE INTERMEDIATE IN COMBINATION WITH GROUND STATE)
KeywordsION TRANSPORT / PHOTO CYCLE INTERMEDIATE / 7-HELICAL MEMBRANE PROTEIN / PROTON TRANSPORT / RETINAL PROTEIN
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
HEXANE / N-OCTANE / RETINAL / TRIDECANE / UNDECANE / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSass, H.J. / Berendzen, J. / Neff, D. / Gessenich, R. / Ormos, P. / Bueldt, G.
CitationJournal: Nature / Year: 2000
Title: Structural alterations for proton translocation in the M state of wild-type bacteriorhodopsin.
Authors: Sass, H.J. / Buldt, G. / Gessenich, R. / Hehn, D. / Neff, D. / Schlesinger, R. / Berendzen, J. / Ormos, P.
History
DepositionAug 26, 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: Version format compliance
Revision 2.0Feb 8, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_distant_solvent_atoms / pdbx_validate_planes / pdbx_validate_torsion / struct_conn / struct_site
Item: _atom_site.label_alt_id / _database_2.pdbx_DOI ..._atom_site.label_alt_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_planes.label_alt_id / _pdbx_validate_torsion.label_alt_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 3.0Jun 12, 2024Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.label_alt_id
Revision 3.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BACTERIORHODOPSIN ("M" STATE INTERMEDIATE IN COMBINATION WITH GROUND STATE)
B: BACTERIORHODOPSIN ("M" STATE INTERMEDIATE IN COMBINATION WITH GROUND STATE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,56446
Polymers53,7772
Non-polymers5,78744
Water2,774154
1
A: BACTERIORHODOPSIN ("M" STATE INTERMEDIATE IN COMBINATION WITH GROUND STATE)
B: BACTERIORHODOPSIN ("M" STATE INTERMEDIATE IN COMBINATION WITH GROUND STATE)
hetero molecules

A: BACTERIORHODOPSIN ("M" STATE INTERMEDIATE IN COMBINATION WITH GROUND STATE)
B: BACTERIORHODOPSIN ("M" STATE INTERMEDIATE IN COMBINATION WITH GROUND STATE)
hetero molecules

A: BACTERIORHODOPSIN ("M" STATE INTERMEDIATE IN COMBINATION WITH GROUND STATE)
B: BACTERIORHODOPSIN ("M" STATE INTERMEDIATE IN COMBINATION WITH GROUND STATE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,693138
Polymers161,3316
Non-polymers17,362132
Water1086
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)61.080, 61.080, 110.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein BACTERIORHODOPSIN ("M" STATE INTERMEDIATE IN COMBINATION WITH GROUND STATE)


Mass: 26888.557 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SCHIFF BASE LINKAGE BETWEEN LYS 216 (NZ) AND RET 601 (C15) DIETHER LIPID BILAYER
Source: (gene. exp.) Halobacterium salinarum (Halophile) / Cellular location: TRANSMEMBRANE / Production host: Halobacterium salinarum (Halophile) / References: UniProt: P02945

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Non-polymers , 6 types, 198 molecules

#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical
ChemComp-UND / UNDECANE / LIPID FRAGMENT


Mass: 156.308 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H24
#4: Chemical
ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C8H18
#5: Chemical
ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H14
#6: Chemical
ChemComp-TRD / TRIDECANE / LIPID FRAGMENT


Mass: 184.361 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C13H28
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE ENTRY CONTAINS THE COORDINATES OF THE M INTERMEDIATE (CHAIN B + LIPID RESIDUES 1604-1624 AND ...THE ENTRY CONTAINS THE COORDINATES OF THE M INTERMEDIATE (CHAIN B + LIPID RESIDUES 1604-1624 AND WATERS 1710-1872) AND THE GROUND STATE STRUCTURE (CHAIN A + LIPID RESIDUES 604-624 AND WATERS 710-872). THE GROUND STATE MODEL WAS REFINED WITH AN OTHER CRYSTAL AND KEPT FIXED DURING THE REFINEMENT OF THE M INTERMEDIATE MODEL. THE CRYSTAL WAS EXCITED BY LIGHT SO THAT ABOUT 35% OF THE PROTEIN IS IN ONE CONFORMATION (CHAIN B) AND 65% IN THE OTHER (CHAIN A).
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: 2.25 Å3/Da / Description: TWINNING OF 38%
Crystal growpH: 5.6 / Details: CUBIC LIPID PHASE 2.5M PHOSPHATE, pH 5.60
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.6 / Method: cubic lipid phase
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: NSLS / Beamline: X8C / Wavelength: 1.214
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 9, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.214 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. obs: 10792 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 22.16 Å2 / Rsym value: 8.2 / Net I/σ(I): 12.05
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3.4 / Rsym value: 32.8 / % possible all: 99.4
Reflection
*PLUS
Rmerge(I) obs: 0.082

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Processing

Software
NameVersionClassification
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→13 Å / Cross valid method: FREE R VALUE, MAXIMUM LIKELIHOOD / σ(F): 1 / Stereochemistry target values: ENGH & HUBER
Details: THE TWIN RATIO OF 0.38 WAS CONSTANT DURING THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 587 5.3 %SHELLS
Rwork0.167 ---
obs0.167 10756 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 138.6 Å2 / ksol: 0.264 e/Å3
Displacement parametersBiso mean: 22.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.907 Å20.123 Å20 Å2
2--0.907 Å20 Å2
3----1.814 Å2
Refinement stepCycle: LAST / Resolution: 2.25→13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3670 0 406 154 4230
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0096
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d1.32
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.1061.5
X-RAY DIFFRACTIONc_mcangle_it1.452
X-RAY DIFFRACTIONc_scbond_it1.7172
X-RAY DIFFRACTIONc_scangle_it1.932.5
LS refinement shellResolution: 2.25→2.33 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.293 69 6.4 %
Rwork0.195 997 -
obs--99.4 %
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 13 Å / % reflection Rfree: 5.3 % / Rfactor obs: 0.179 / Rfactor Rfree: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.293 / Rfactor Rwork: 0.195

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