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- PDB-1gu8: SENSORY RHODOPSIN II -

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Basic information

Entry
Database: PDB / ID: 1gu8
TitleSENSORY RHODOPSIN II
ComponentsSENSORY RHODOPSIN II
KeywordsMEMBRANE PROTEIN / ARCHAEAL RHODOPSIN / PHOTORECEPTOR / PHOTOTAXIS
Function / homology
Function and homology information


photoreceptor activity / phototransduction / monoatomic ion channel activity / 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 / Sensory rhodopsin-2
Similarity search - Component
Biological speciesNATRONOMONAS PHARAONIS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsEdman, K. / Royant, A. / Nollert, P. / Maxwell, C.A. / Pebay-Peyroula, E. / Navarro, J. / Neutze, R. / Landau, E.M.
CitationJournal: Structure / Year: 2002
Title: Early Structural Rearrangements in the Photocycle of an Integral Membrane Sensory Receptor
Authors: Edman, K. / Royant, A. / Nollert, P. / Maxwell, C.A. / Pebay-Peyroula, E. / Navarro, J. / Neutze, R. / Landau, E.M.
History
DepositionJan 24, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2002Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SENSORY RHODOPSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6893
Polymers25,3691
Non-polymers3202
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.510, 128.553, 50.799
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Number of models2

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Components

#1: Protein SENSORY RHODOPSIN II / / SR-II


Mass: 25368.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MODEL 1 - GROUND STATE, MODEL 2 - K-STATE / Source: (gene. exp.) NATRONOMONAS PHARAONIS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P42196
#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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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: 2.75 Å3/Da / Density % sol: 53 %
Description: SIDE CHAINS, LOOPS AND THE RETINAL WERE OMITTED IN THE STARTING MODEL FOR MOLECULAR REPLACEMENT. LOOPS AB AND CD WERE RESTRAINED IN THE PARTIAL OCCUPANCY REFINEMENT.
Crystal growpH: 4.6 / Details: pH 4.6
Crystal grow
*PLUS
Method: unknown
Details: Royant, A., (2001) Proc. Natl. Acad. Sci. U.S.A., 98, 10131.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14.5 mg/mlprotein11
20.005 %n-dodecyl beta-D-maltoside11
375 mM11NaOAc
41.5 M11NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.27→35.6 Å / Num. obs: 13086 / % possible obs: 99.4 % / Redundancy: 5.8 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 11.5
Reflection shellResolution: 2.27→2.38 Å / Redundancy: 5 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 1.9 / % possible all: 98.1
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 36 Å / Num. measured all: 76030
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 98.1 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
CCP4data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H68

1h68


Resolution: 2.27→36 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 735 5.6 %RANDOM
Rwork0.23 ---
obs0.23 13075 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 81.5 Å2 / ksol: 0.46 e/Å3
Displacement parametersBiso mean: 29.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.12 Å20 Å20 Å2
2--3.85 Å20 Å2
3----6.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.27→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1621 0 21 16 1658
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it1.822
X-RAY DIFFRACTIONc_scbond_it1.792
X-RAY DIFFRACTIONc_scangle_it2.272.5
LS refinement shellResolution: 2.27→2.41 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.253 116 5.8 %
Rwork0.259 1879 -
obs--91.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3RET-CIS.PARRET.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
% reflection Rfree: 5.5 % / Rfactor obs: 0.23 / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.23 / Highest resolution: 2.3 Å / Lowest resolution: 36 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0074
X-RAY DIFFRACTIONc_angle_deg1.14
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
LS refinement shell
*PLUS
Rfactor obs: 0.259

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