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- PDB-1h68: sensory rhodopsin II -

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Basic information

Entry
Database: PDB / ID: 1h68
Titlesensory rhodopsin II
ComponentsSENSORY RHODOPSIN II
KeywordsRECEPTOR / ARCHAEAL RHODOPSIN / PHOTORECEPTOR / PHOTOTAXIS
Function / homology
Function and homology information


monoatomic ion channel activity / photoreceptor activity / phototransduction / 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: 2.1 Å
AuthorsRoyant, A. / Nollert, P. / Edman, K. / Neutze, R. / Landau, E.M. / Pebay-Peyroula, E. / Navarro, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: X-Ray Structure of Sensory Rhodopsin II at 2.1 A Resolution
Authors: Royant, A. / Nollert, P. / Edman, K. / Neutze, R. / Landau, E.M. / Pebay-Peyroula, E. / Navarro, J.
History
DepositionJun 8, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 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: SENSORY RHODOPSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6893
Polymers25,3691
Non-polymers3202
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)84.830, 128.740, 50.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein SENSORY RHODOPSIN II / SRII


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


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


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


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.95 %
Description: SIDE CHAINS, LOOPS AND THE RETINAL WERE OMITTED IN THE STARTING MODEL FOR MOLECULAR REPLACEMENT
Crystal growpH: 4.6 / Details: pH 4.60
Crystal grow
*PLUS
Method: unknown
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: ID14-2 / Wavelength: 0.933
DetectorDate: Oct 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.1→39.9 Å / Num. obs: 15956 / % possible obs: 96.1 % / Redundancy: 6.3 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 8.4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 1.8 / % possible all: 80.1
Reflection
*PLUS
Num. measured all: 99617
Reflection shell
*PLUS
% possible obs: 80.1 %

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Processing

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

1qhj


Resolution: 2.1→39.9 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 891 5.6 %RANDOM
Rwork0.237 ---
obs0.237 15956 95.8 %-
Solvent computationSolvent model: FALT MODEL / Bsol: 113.25 Å2 / ksol: 0.48 e/Å3
Displacement parametersBiso mean: 37.5 Å2
Baniso -1Baniso -2Baniso -3
1-7.55 Å20 Å20 Å2
2--3.4 Å20 Å2
3----10.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.1→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1625 0 21 28 1674
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it5.62
X-RAY DIFFRACTIONc_scangle_it6.862.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 109 5 %
Rwork0.273 2059 -
obs--80.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3RETFIN-LO.PARRETFIN.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74

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