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- PDB-7u55: Crystal structure of Thermoplasmatales archaeon heliorhodopsin at... -

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Basic information

Entry
Database: PDB / ID: 7u55
TitleCrystal structure of Thermoplasmatales archaeon heliorhodopsin at pH 4.5
ComponentsHeliorhodopsin
KeywordsMEMBRANE PROTEIN / microbial rhodopsin / retinal protein / heliorhodopsin / seven transmembrane protein
Function / homologyHeliorhodopsin / Heliorhodopsin / identical protein binding / membrane / DODECANE / RETINAL / Heliorhodopsin HeR
Function and homology information
Biological speciesThermoplasmatales archaeon SG8-52-1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsBesaw, J.E. / De Guzman, P. / Miller, R.J.D. / Ernst, O.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2017-06862 Canada
CitationJournal: Sci Rep / Year: 2022
Title: Low pH structure of heliorhodopsin reveals chloride binding site and intramolecular signaling pathway.
Authors: Besaw, J.E. / Reichenwallner, J. / De Guzman, P. / Tucs, A. / Kuo, A. / Morizumi, T. / Tsuda, K. / Sljoka, A. / Miller, R.J.D. / Ernst, O.P.
History
DepositionMar 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)30,4125
Polymers29,8861
Non-polymers5264
Water66737
1
A: Heliorhodopsin
hetero molecules

A: Heliorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,82410
Polymers59,7732
Non-polymers1,0518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7360 Å2
ΔGint-77 kcal/mol
Surface area20060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.848, 47.974, 56.688
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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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)
Gene: AYK20_03510 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A151EDA9
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.04 Å3/Da / Density % sol: 39.82 % / Description: Diamond
Crystal growTemperature: 307.15 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Bicelle crystallization with 5 mg/mL protein in 8% bicelle (2.8:1 DMPC:CHAPSO). Crystallization condition is 26% polyethylene glycol 3350, 0.1 M sodium phosphate monobasic monohydrate at pH ...Details: Bicelle crystallization with 5 mg/mL protein in 8% bicelle (2.8:1 DMPC:CHAPSO). Crystallization condition is 26% polyethylene glycol 3350, 0.1 M sodium phosphate monobasic monohydrate at pH 4.5, 0.28 M ammonium sulfate, 0.18 M 1,6-hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.97→47.94 Å / Num. obs: 16754 / % possible obs: 94.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 22.85 Å2 / CC1/2: 0.98 / Net I/σ(I): 4.3
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1100 / CC1/2: 0.72 / % possible all: 89.2

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6is6

6is6


Resolution: 1.97→47.94 Å / SU ML: 0.1674 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.3999
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2226 1671 10 %
Rwork0.1979 15033 -
obs0.2003 16704 93.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.56 Å2
Refinement stepCycle: LAST / Resolution: 1.97→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1983 0 34 37 2054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00872135
X-RAY DIFFRACTIONf_angle_d1.13282917
X-RAY DIFFRACTIONf_chiral_restr0.0679338
X-RAY DIFFRACTIONf_plane_restr0.008354
X-RAY DIFFRACTIONf_dihedral_angle_d20.7872756
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.030.29721300.24571172X-RAY DIFFRACTION89.12
2.03-2.10.24081410.21711269X-RAY DIFFRACTION95.66
2.1-2.170.21611420.19051274X-RAY DIFFRACTION96.59
2.17-2.260.2271390.18121263X-RAY DIFFRACTION96.42
2.26-2.360.18611410.17321272X-RAY DIFFRACTION95.8
2.36-2.480.20871390.16681260X-RAY DIFFRACTION94.65
2.48-2.640.211380.16651237X-RAY DIFFRACTION93.92
2.64-2.840.19921400.17361256X-RAY DIFFRACTION93.57
2.84-3.130.19711400.18231252X-RAY DIFFRACTION93.61
3.13-3.580.18791390.19371247X-RAY DIFFRACTION92.15
3.58-4.510.2281380.21031245X-RAY DIFFRACTION91.11
4.51-47.940.26031440.22581286X-RAY DIFFRACTION88

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