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- PDB-6jyc: Structure of dark-state marine bacterial chloride importer, NM-R3... -

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Basic information

Entry
Database: PDB / ID: 6jyc
TitleStructure of dark-state marine bacterial chloride importer, NM-R3, with CW laser (ND-30%) at 95K.
ComponentsChloride pumping rhodopsin
KeywordsMEMBRANE PROTEIN / Photo-excitation / Chloride pump / Retinal
Function / homology
Function and homology information


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
OLEIC ACID / RETINAL / Chloride pumping rhodopsin
Similarity search - Component
Biological speciesNonlabens marinus S1-08 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.892 Å
AuthorsYun, J.H. / Ohki, M. / Park, S.Y. / Lee, W.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2017R1A2B2008483 Korea, Republic Of
National Research Foundation (Korea)NRF-2016R1A6A3A04010213 Korea, Republic Of
CitationJournal: Sci Adv / Year: 2020
Title: Pumping mechanism of NM-R3, a light-driven bacterial chloride importer in the rhodopsin family.
Authors: Yun, J.H. / Ohki, M. / Park, J.H. / Ishimoto, N. / Sato-Tomita, A. / Lee, W. / Jin, Z. / Tame, J.R.H. / Shibayama, N. / Park, S.Y. / Lee, W.
History
DepositionApr 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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: Chloride pumping rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,37615
Polymers32,9131
Non-polymers3,46214
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-10 kcal/mol
Surface area12100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.539, 49.213, 69.186
Angle α, β, γ (deg.)90.00, 110.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Chloride pumping rhodopsin


Mass: 32913.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nonlabens marinus S1-08 (bacteria) / Strain: S1-08 / Gene: ClR, NMS_1267 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: W8VZW3
#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: C18H34O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 30% polyethylene glycol dimethyl ether 500, 0.15 M sodium chloride, 0.15M calcium chloride, and 0.1 M MES (pH 6.0) buffer

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.892→47.205 Å / Num. obs: 24583 / % possible obs: 95 % / Redundancy: 4.6 % / Net I/σ(I): 15.5
Reflection shellResolution: 1.9→1.93 Å

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZTK

5ztk


Resolution: 1.892→47.205 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 20.14
RfactorNum. reflection% reflection
Rfree0.21 1256 5.11 %
Rwork0.1677 --
obs0.1699 24576 94.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.892→47.205 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2072 0 150 93 2315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042262
X-RAY DIFFRACTIONf_angle_d0.7883036
X-RAY DIFFRACTIONf_dihedral_angle_d12.68818
X-RAY DIFFRACTIONf_chiral_restr0.026342
X-RAY DIFFRACTIONf_plane_restr0.004362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8923-1.96810.30271000.25152155X-RAY DIFFRACTION78
1.9681-2.05770.30431250.21482393X-RAY DIFFRACTION89
2.0577-2.16620.22251410.18352595X-RAY DIFFRACTION95
2.1662-2.30190.20151410.1562630X-RAY DIFFRACTION97
2.3019-2.47960.18481390.14922668X-RAY DIFFRACTION97
2.4796-2.72910.17021360.14862681X-RAY DIFFRACTION97
2.7291-3.12390.21421540.15312664X-RAY DIFFRACTION97
3.1239-3.93550.1891610.15542731X-RAY DIFFRACTION99
3.9355-47.21990.21361590.17382803X-RAY DIFFRACTION99

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