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- PDB-6is6: Crystal structure of Thermoplasmatales archaeon heliorhodopsin -

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Basic information

Entry
Database: PDB / ID: 6is6
TitleCrystal structure of Thermoplasmatales archaeon heliorhodopsin
Componentsheliorhodopsin
KeywordsMEMBRANE PROTEIN / alpha-helical
Function / homologyHeliorhodopsin / Heliorhodopsin / membrane / identical protein binding / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Heliorhodopsin HeR
Function and homology information
Biological speciesThermoplasmatales archaeon SG8-52-1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsShihoya, W. / Yamashita, K. / Nureki, O.
CitationJournal: Nature / Year: 2019
Title: Crystal structure of heliorhodopsin.
Authors: Shihoya, W. / Inoue, K. / Singh, M. / Konno, M. / Hososhima, S. / Yamashita, K. / Ikeda, K. / Higuchi, A. / Izume, T. / Okazaki, S. / Hashimoto, M. / Mizutori, R. / Tomida, S. / Yamauchi, Y. ...Authors: Shihoya, W. / Inoue, K. / Singh, M. / Konno, M. / Hososhima, S. / Yamashita, K. / Ikeda, K. / Higuchi, A. / Izume, T. / Okazaki, S. / Hashimoto, M. / Mizutori, R. / Tomida, S. / Yamauchi, Y. / Abe-Yoshizumi, R. / Katayama, K. / Tsunoda, S.P. / Shibata, M. / Furutani, Y. / Pushkarev, A. / Beja, O. / Uchihashi, T. / Kandori, H. / Nureki, O.
History
DepositionNov 15, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 20, 2019Group: Source and taxonomy / Structure summary / Category: entity_src_gen / pdbx_entry_details
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_entry_details.sequence_details
Revision 1.4Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: heliorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,16216
Polymers29,8861
Non-polymers5,27615
Water55831
1
A: heliorhodopsin
hetero molecules

A: heliorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,32532
Polymers59,7732
Non-polymers10,55230
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area6270 Å2
ΔGint-46 kcal/mol
Surface area22460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.980, 109.350, 107.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein heliorhodopsin /


Mass: 29886.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasmatales archaeon SG8-52-1 (archaea)
Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Variant (production host): C41(Rosetta) / References: UniProt: A0A151EDA9
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
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: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8
Details: 30% PEG 350MME, 100mM Tris-HCl, pH 8.0, 100mM potassium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 18, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→48.773 Å / Num. obs: 12404 / % possible obs: 99.9 % / Redundancy: 35.302 % / Biso Wilson estimate: 32.63 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.324 / Rrim(I) all: 0.328 / Χ2: 1.218 / Net I/σ(I): 13.68 / Num. measured all: 437886 / Scaling rejects: 318
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.5535.5752.4722.1620100.5082.506100
2.55-2.7236.3081.3873.518020.7081.406100
2.72-2.9436.3730.8525.5717430.9270.86399.9
2.94-3.2235.820.5677.9315970.9680.574100
3.22-3.634.9670.33913.1414590.9820.344100
3.6-4.1632.4960.20421.5713000.9930.207100
4.16-5.0933.5360.14232.2610970.9940.14499.3
5.09-7.236.9820.10532.318760.9980.10699.9
7.2-48.77334.4270.06249.6752010.06399

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AX0

5ax0


Resolution: 2.4→48.773 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.09
RfactorNum. reflection% reflection
Rfree0.2254 618 5 %
Rwork0.189 --
obs0.1908 12361 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 102.23 Å2 / Biso mean: 39.1079 Å2 / Biso min: 18.45 Å2
Refinement stepCycle: final / Resolution: 2.4→48.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 352 31 2397
Biso mean--53.51 36.38 -
Num. residues----250
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4002-2.64170.28441530.19492887100
2.6417-3.0240.26731540.18582894100
3.024-3.80960.21321520.1892922100
3.8096-48.7730.20661590.1884304099

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