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- PDB-6guy: Room temperature structure of Archaerhodopsin-3 via LCP extruder ... -

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Basic information

Entry
Database: PDB / ID: 6guy
TitleRoom temperature structure of Archaerhodopsin-3 via LCP extruder using synchrotron radiation
ComponentsArchaerhodopsin-3
KeywordsPROTON TRANSPORT / Membrane Protein / Rhodopsin / LCP extruder / Room temperature / synchrotron
Function / homology
Function and homology information


photoreceptor activity / phototransduction / proton transmembrane transport / 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
nonane / HEXADECANE / RETINAL / Archaerhodopsin-3
Similarity search - Component
Biological speciesHalorubrum sodomense (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMoraes, I. / Judge, P.J. / Axford, D. / Bada Juarez, J.F. / Vinals, J. / Watts, A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust202892/Z/16/Z United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/N006011/1 United Kingdom
CitationJournal: To Be Published
Title: Room temperature structure of Archaerhodopsin-3 via LCP extruder using synchrotron radiation
Authors: Bada Juarez, J.F. / Judge, P.J. / Vinals, J. / Axford, D. / Birch, J. / Aller, P. / Butryn, A. / Owen, R.L. / Sherrell, D.A. / Beale, J.H. / Orville, A.M. / Watts, A. / Moraes, I.
History
DepositionJun 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 2.0Mar 11, 2020Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Archaerhodopsin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,38817
Polymers26,1611
Non-polymers2,22716
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, Homology to bacteriorhodopsin
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-59 kcal/mol
Surface area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.294, 48.271, 104.902
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Archaerhodopsin-3 / AR 3


Mass: 26160.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halorubrum sodomense (archaea) / Tissue: MEMBRANE / References: UniProt: P96787

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Non-polymers , 7 types, 59 molecules

#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-R16 / HEXADECANE


Mass: 226.441 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C16H34
#4: Chemical
ChemComp-DD9 / nonane


Mass: 128.255 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H20
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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 / Density % sol: 45.33 % / Description: plates
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.5
Details: 100mM MES pH 5.5, 33% PEG 600, 150mM Na chloride, 150mM Ca chloride

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 2.2→28.3203 Å / Num. obs: 12478 / % possible obs: 100 % / Redundancy: 31.3 % / Biso Wilson estimate: 37.08 Å2 / CC1/2: 0.937 / R split: 0.2 / Rmerge(I) obs: 0.715 / Net I/σ(I): 2.16
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.888 / Mean I/σ(I) obs: 0.47 / Num. unique obs: 600 / CC1/2: 0.535 / R split: 0.7623 / % possible all: 100
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionInjector nozzle: 75 microns

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
DIALS1.5.0data reduction
cctbx.primedata scaling
PHASER2.7.17phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UAZ

1uaz


Resolution: 2.2→28.3203 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.42
RfactorNum. reflection% reflection
Rfree0.2521 1246 9.99 %
Rwork0.2229 --
obs0.2259 12469 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.84 Å2 / Biso mean: 39.6128 Å2 / Biso min: 22.25 Å2
Refinement stepCycle: final / Resolution: 2.2→28.3203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1831 0 162 43 2036
Biso mean--45.81 44.11 -
Num. residues----241
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.28810.35831260.34261223100
2.2881-2.39220.35741390.30821222100
2.3922-2.51820.37541330.30451211100
2.5182-2.67590.3011410.27851250100
2.6759-2.88230.27591270.23021234100
2.8823-3.1720.27621470.2231226100
3.172-3.63020.24131400.20571242100
3.6302-4.57050.20151440.16871276100
4.5705-28.320.20931490.2015133999

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