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- PDB-7zy3: Room temperature structure of Archaerhodopsin-3 obtained 110 ns a... -

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Basic information

Entry
Database: PDB / ID: 7zy3
TitleRoom temperature structure of Archaerhodopsin-3 obtained 110 ns after photoexcitation
ComponentsArchaerhodopsin-3
KeywordsPROTON TRANSPORT / Membrane protein / Proton tranport / Rhodopsin / Lipidic cubic phase / SFX
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
Similarity search - Domain/homology
nonane / PALMITIC ACID / HEXADECANE / RETINAL / Archaerhodopsin-3
Similarity search - Component
Biological speciesHalorubrum sodomense (archaea)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKwan, T.O.C. / Judge, P.J. / Moraes, I. / Watts, A. / Axford, D. / Bada Juarez, J.F.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Other government
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N006011/1 United Kingdom
Wellcome Trust202892/Z/16/Z United Kingdom
CitationJournal: J.Appl.Crystallogr. / Year: 2023
Title: A versatile approach to high-density microcrystals in lipidic cubic phase for room-temperature serial crystallography.
Authors: Birch, J. / Kwan, T.O.C. / Judge, P.J. / Axford, D. / Aller, P. / Butryn, A. / Reis, R.I. / Bada Juarez, J.F. / Vinals, J. / Owen, R.L. / Nango, E. / Tanaka, R. / Tono, K. / Joti, Y. / ...Authors: Birch, J. / Kwan, T.O.C. / Judge, P.J. / Axford, D. / Aller, P. / Butryn, A. / Reis, R.I. / Bada Juarez, J.F. / Vinals, J. / Owen, R.L. / Nango, E. / Tanaka, R. / Tono, K. / Joti, Y. / Tanaka, T. / Owada, S. / Sugahara, M. / Iwata, S. / Orville, A.M. / Watts, A. / Moraes, I.
History
DepositionMay 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)28,44812
Polymers27,1031
Non-polymers1,34611
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-47 kcal/mol
Surface area10830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.200, 48.300, 104.700
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: 27102.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The PCA residue needs to be in position 7 in the protein chain as the PCA is a modified glutamine residue, so Gln7 has become PCA.
Source: (natural) Halorubrum sodomense (archaea) / Variant: RD-26 / Tissue: MEMBRANE / References: UniProt: P96787

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Non-polymers , 9 types, 74 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-DD9 / nonane


Mass: 128.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20
#4: Chemical ChemComp-R16 / HEXADECANE


Mass: 226.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34
#5: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#6: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.32 Å3/Da / Density % sol: 47 % / Description: Plates
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.5
Details: 33% v/v polyethylene glycol 600, 100 mM MES buffer pH 5.5, 150 mM NaCl and 150 mM CaCl2

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.23 Å
DetectorType: MPCCD / Detector: CCD / Date: Jan 31, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23 Å / Relative weight: 1
ReflectionResolution: 1.7→28.29 Å / Num. obs: 26515 / % possible obs: 100 % / Redundancy: 101.5 % / Biso Wilson estimate: 32.3 Å2 / CC1/2: 0.992 / Net I/σ(I): 3.79
Reflection shellResolution: 1.7→1.72 Å / Redundancy: 65.2 % / Mean I/σ(I) obs: 0.59 / Num. unique obs: 1299 / R split: 1.82 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
DIALS1.10.1data scaling
PHASERv3.24phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AUZ

1auz


Resolution: 1.8→28.149 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1818 1080 4.82 %
Rwork0.1654 21317 -
obs0.1663 22397 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.25 Å2 / Biso mean: 37.1892 Å2 / Biso min: 16.02 Å2
Refinement stepCycle: final / Resolution: 1.8→28.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1793 0 279 66 2138
Biso mean--54.55 47.34 -
Num. residues----238
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.8-1.88190.29221400.26812602
1.8819-1.98110.31881100.24132635
1.9811-2.10520.24631290.18142647
2.1052-2.26770.18581750.14072585
2.2677-2.49570.15451160.13012667
2.4957-2.85660.16611400.12182654
2.8566-3.59780.17091260.14312704
3.5978-28.140.16911440.19442823

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