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- PDB-6uh3: Crystal structure of bacterial heliorhodopsin 48C12 -

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Basic information

Entry
Database: PDB / ID: 6uh3
TitleCrystal structure of bacterial heliorhodopsin 48C12
ComponentsHeliorhodopsin
KeywordsSIGNALING PROTEIN / Heliorhodopsin / bacterium
Function / homologyHeliorhodopsin / Heliorhodopsin / membrane / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PALMITIC ACID / RETINAL / Heliorhodopsin
Function and homology information
Biological speciesActinobacteria bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLu, Y. / Zhou, X.E. / Gao, X. / Xia, R. / Xu, Z. / Wang, N. / Leng, Y. / Melcher, K. / Xu, H.E. / He, Y.
CitationJournal: Cell Res. / Year: 2020
Title: Crystal structure of heliorhodopsin 48C12.
Authors: Lu, Y. / Zhou, X.E. / Gao, X. / Wang, N. / Xia, R. / Xu, Z. / Leng, Y. / Shi, Y. / Wang, G. / Melcher, K. / Xu, H.E. / He, Y.
History
DepositionSep 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Structure summary / Category: citation_author / struct / Item: _struct.pdbx_descriptor
Revision 1.2Jan 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.4Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Heliorhodopsin
B: Heliorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,27231
Polymers55,3112
Non-polymers4,96029
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10090 Å2
ΔGint-35 kcal/mol
Surface area24480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.449, 102.139, 56.770
Angle α, β, γ (deg.)90.000, 94.040, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 253 or resid 301))
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 5 through 253 or resid 301))A0
211chain BB5 - 253

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Heliorhodopsin / Heliorhodopsin 48C12


Mass: 27655.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinobacteria bacterium (bacteria) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A2R4S913

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Non-polymers , 5 types, 65 molecules

#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H32O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.54 Å3/Da / Density % sol: 51.55 %
Crystal growTemperature: 273 K / Method: lipidic cubic phase / pH: 5.4
Details: 50 mM sodium citrate tribasic dihydrate, pH 5.4, 350 mM potassium citrate tribasic monohydrate, 37% PEG400, 0.5% w/v DDM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 11, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 14449 / % possible obs: 95.9 % / Redundancy: 3.3 % / CC1/2: 0.942 / Net I/σ(I): 4.8
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 3.1 % / Num. unique obs: 1858 / CC1/2: 0.31 / % possible all: 91

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3AM6

3am6


Resolution: 2.7→49 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.06
RfactorNum. reflection% reflection
Rfree0.2793 1032 7.18 %
Rwork0.2641 --
obs0.2652 14372 93.3 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 191.69 Å2 / Biso mean: 36.6421 Å2 / Biso min: 8.28 Å2
Refinement stepCycle: final / Resolution: 2.7→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3822 0 332 36 4190
Biso mean--46.67 38.32 -
Num. residues----491
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2226X-RAY DIFFRACTION8.759TORSIONAL
12B2226X-RAY DIFFRACTION8.759TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7-2.84240.34551600.3243181890
2.8424-3.02040.30911380.31186291
3.0204-3.25360.31451510.3025189293
3.2536-3.58090.31941460.2862181889
3.5809-4.09890.25461440.2461200797
4.0989-5.16330.23091670.2183197496
5.1633-490.26281260.2486196993

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