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- PDB-4tl3: Mechanistic insights from the crystal structure of an inward prot... -

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Basic information

Entry
Database: PDB / ID: 4tl3
TitleMechanistic insights from the crystal structure of an inward proton-transporting Anabaena sensory rhodopsin mutant
ComponentsAnabaena sensory rhodopsin
KeywordsSIGNALING PROTEIN / transmembrane / photoreceptor / proton pump / bacterial rhodopsin
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. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDong, B.H. / Luecke, H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM067808 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI078000 United States
UC Irvine Center for Biomembrane Systems United States
CitationJournal: To Be Published
Title: Mechanistic insights from the crystal structure of an inward proton-transportingAnabaena sensory rhodopsin mutant
Authors: Dong, B.H. / Luecke, H.
History
DepositionMay 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Non-polymer description
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Sep 27, 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 / refine_hist / struct_ncs_dom_lim
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 / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anabaena sensory rhodopsin
B: Anabaena sensory rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,72539
Polymers52,1152
Non-polymers26,61037
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18000 Å2
ΔGint-106 kcal/mol
Surface area18680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.265, 104.301, 111.386
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 0 / Auth seq-ID: 1 - 226 / Label seq-ID: 1 - 226

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Anabaena sensory rhodopsin


Mass: 26057.576 Da / Num. of mol.: 2 / Mutation: D217E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / UTEX 2576 / Gene: alr3165 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YSC4
#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 2 / 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.: 35 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.06 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.6 / Details: MPD, pH 5.6, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2013
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.3→33.19 Å / Num. obs: 28486 / % possible obs: 96.7 % / Redundancy: 1.93 % / Net I/σ(I): 11.4
Reflection shellResolution: 2.3→2.34 Å / Mean I/σ(I) obs: 2 / % possible all: 98.7

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Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XIO

1xio


Resolution: 2.3→33.19 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.228 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24951 1449 5.1 %RANDOM
Rwork0.21976 ---
obs0.22137 26889 96.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.739 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.3→33.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3556 0 475 109 4140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.024118
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2032.0145446
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7365429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23422.245147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90915583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.811516
X-RAY DIFFRACTIONr_chiral_restr0.0860.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212788
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0332.351728
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7093.5132153
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3652.9362390
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.60621.7886633
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 314 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 98 -
Rwork0.256 1970 -
obs--98.66 %

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