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- PDB-1xio: Anabaena sensory rhodopsin -

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Basic information

Entry
Database: PDB / ID: 1xio
TitleAnabaena sensory rhodopsin
ComponentsANABAENA SENSORY RHODOPSIN
KeywordsSIGNALING PROTEIN / photoreceptor
Function / homology
Function and homology information


photoreceptor activity / phototransduction / monoatomic ion channel activity / membrane
Similarity search - Function
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
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVogeley, L. / Luecke, H.
CitationJournal: Science / Year: 2004
Title: Anabaena sensory rhodopsin: a photochromic color sensor at 2.0 A.
Authors: Vogeley, L. / Sineshchekov, O.A. / Trivedi, V.D. / Sasaki, J. / Spudich, J.L. / Luecke, H.
History
DepositionSep 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 29, 2014Group: Non-polymer description
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type
Revision 2.0Aug 23, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.mon_nstd_flag / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _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 600HETEROGEN PEE IS POSSIBLY A FRAGMENT OF PHOSPHATIDYLETHANOLAMINE. THE REST OF THE MOLECULE WAS NOT ...HETEROGEN PEE IS POSSIBLY A FRAGMENT OF PHOSPHATIDYLETHANOLAMINE. THE REST OF THE MOLECULE WAS NOT VISIBLE IN THE ELECTRON DENSITY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANABAENA SENSORY RHODOPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,17315
Polymers30,2161
Non-polymers9,95714
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: ANABAENA SENSORY RHODOPSIN
hetero molecules

A: ANABAENA SENSORY RHODOPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,34630
Polymers60,4322
Non-polymers19,91428
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area17210 Å2
ΔGint-107 kcal/mol
Surface area17440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.095, 116.513, 56.186
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 ANABAENA SENSORY RHODOPSIN


Mass: 30216.170 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CONTAINS 6XHIS-TAG, RESIDUES 1-229 / Source: (gene. exp.) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC7120 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YSC4
#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical
ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE / Discrete optimized protein energy


Mass: 744.034 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.79 Å3/Da / Density % sol: 55.94 %
Crystal growTemperature: 293 K / Method: cubic lipid phase / pH: 5.6 / Details: MPD, pH 5.6, cubic lipid phase, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.8984 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8984 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 23141 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.097 / Χ2: 0.914 / Net I/σ(I): 18
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2149 / Χ2: 0.837 / % possible all: 93.8

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Processing

Software
NameClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JGJ

1jgj


Resolution: 2→30 Å / Data cutoff low absF: 0 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2559 1574 6.8 %random
Rwork0.2296 ---
obs-20239 87 %-
Solvent computationBsol: 56.88 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso mean: 21.89 Å2
Baniso -1Baniso -2Baniso -3
1-4.297 Å20 Å20 Å2
2---1.205 Å20 Å2
3----3.093 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1781 0 217 80 2078
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1181.5
X-RAY DIFFRACTIONc_mcangle_it1.5972
X-RAY DIFFRACTIONc_scbond_it1.7632
X-RAY DIFFRACTIONc_scangle_it2.3112.5
X-RAY DIFFRACTIONc_bond_d0.0071
X-RAY DIFFRACTIONc_angle_deg1.0512
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.parawater.top
X-RAY DIFFRACTION3CRET3.parCRET2.top
X-RAY DIFFRACTION4ion.paramion.top

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