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- PDB-5ztk: Synchrotron structure of light-driven chloride pump having an NTQ... -

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Basic information

Entry
Database: PDB / ID: 5ztk
TitleSynchrotron structure of light-driven chloride pump having an NTQ motif
ComponentsChloride pumping rhodopsin
KeywordsSIGNALING PROTEIN / Chloride pump
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: 1.75 Å
AuthorsYun, J.H. / Park, J.H. / 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: J. Biol. Chem. / Year: 2019
Title: Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency
Authors: Yun, J.H. / Li, X. / Park, J.H. / Wang, Y. / Ohki, M. / Jin, Z. / Lee, W. / Park, S.Y. / Hu, H. / Li, C. / Zatsepin, N. / Hunter, M.S. / Sierra, R.G. / Koralek, J. / Yoon, C.H. / Cho, H.S. / ...Authors: Yun, J.H. / Li, X. / Park, J.H. / Wang, Y. / Ohki, M. / Jin, Z. / Lee, W. / Park, S.Y. / Hu, H. / Li, C. / Zatsepin, N. / Hunter, M.S. / Sierra, R.G. / Koralek, J. / Yoon, C.H. / Cho, H.S. / Weierstall, U. / Tang, L. / Liu, H. / Lee, W.
History
DepositionMay 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 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)32,82211
Polymers30,4901
Non-polymers2,33310
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-14 kcal/mol
Surface area11300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.756, 49.402, 69.327
Angle α, β, γ (deg.)90.00, 109.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Chloride pumping rhodopsin


Mass: 30489.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nonlabens marinus S1-08 (bacteria) / Gene: ClR, NMS_1267 / Production host: Escherichia coli (E. coli) / References: UniProt: W8VZW3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#4: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C18H34O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.52 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 294 K / Method: lipidic cubic phase / pH: 6
Details: 30% PEG 500 DME, 0.1M sodium chloride, 0.1M MES (pH 6.0)

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→23.63 Å / Num. obs: 32667 / % possible obs: 98.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 20.92 Å2 / Net I/σ(I): 24.47
Reflection shellResolution: 1.75→1.81 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
Cootmodel building
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G28

5g28


Resolution: 1.75→23.63 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.911 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.098 / SU Rfree Blow DPI: 0.097 / SU Rfree Cruickshank DPI: 0.099
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1655 5.07 %RANDOM
Rwork0.185 ---
obs0.187 32667 98.4 %-
Displacement parametersBiso mean: 23.12 Å2
Baniso -1Baniso -2Baniso -3
1-1.4461 Å20 Å2-1.1904 Å2
2---8.0235 Å20 Å2
3---6.5774 Å2
Refine analyzeLuzzati coordinate error obs: 0 Å
Refinement stepCycle: 1 / Resolution: 1.75→23.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2072 0 121 72 2265
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012237HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.933013HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d778SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes36HARMONIC2
X-RAY DIFFRACTIONt_gen_planes323HARMONIC5
X-RAY DIFFRACTIONt_it2237HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.06
X-RAY DIFFRACTIONt_other_torsion16.19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion287SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2803SEMIHARMONIC4
LS refinement shellResolution: 1.75→1.81 Å / Rfactor Rfree error: 0 / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.223 164 5.58 %
Rwork0.178 2776 -
all0.181 2940 -
obs--97.08 %

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