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- PDB-6k6k: The crystal structure of light-driven cyanobacterial chloride imp... -

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Basic information

Entry
Database: PDB / ID: 6k6k
TitleThe crystal structure of light-driven cyanobacterial chloride importer (N63A/P118A) Mastigocladopsis repens
ComponentsCyanobacterial chloride importer
KeywordsMEMBRANE PROTEIN / chloride ion pump / rhodopsin
Function / homologyRhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha / OLEIC ACID / RETINAL
Function and homology information
Biological speciesMastigocladopsis repens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.197 Å
AuthorsYun, J.H. / Park, J.H. / Jin, Z. / Ohki, M. / Wang, Y. / Lupala, C.S. / Kim, M. / Liu, H. / Park, S.Y. / Lee, W.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)20171A2B2008483 Korea, Republic Of
National Research Foundation (Korea)20161A6A3A04010213 Korea, Republic Of
CitationJournal: To Be Published
Title: The crystal structure of light-driven cyanobacterial chloride importer (N63A/P118A) Mastigocladopsis repens
Authors: Yun, J.H. / Park, J.H. / Jin, Z. / Ohki, M. / Wang, Y. / Lupala, C.S. / Kim, M. / Liu, H. / Park, S.Y. / Lee, W.
History
DepositionJun 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 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: Cyanobacterial chloride importer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4778
Polymers25,9911
Non-polymers1,4857
Water93752
1
A: Cyanobacterial chloride importer
hetero molecules

A: Cyanobacterial chloride importer
hetero molecules

A: Cyanobacterial chloride importer
hetero molecules


  • defined by author&software
  • Evidence: gel filtration, The buried subunit interface area was analyzed using the PISA interface. Additionally, analytical size exclusion gel chromatography (aSEC) was also used to confirm that the ...Evidence: gel filtration, The buried subunit interface area was analyzed using the PISA interface. Additionally, analytical size exclusion gel chromatography (aSEC) was also used to confirm that the trimeric form was the only species found in solution.
  • 82.4 kDa, 3 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)82,43024
Polymers77,9743
Non-polymers4,45621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area14010 Å2
ΔGint-125 kcal/mol
Surface area26200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.972, 60.972, 205.574
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-420-

HOH

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Components

#1: Protein Cyanobacterial chloride importer


Mass: 25991.463 Da / Num. of mol.: 1 / Mutation: N63A/P118A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mastigocladopsis repens (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H34O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsResidues N63A/P118A represent mutations.

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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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 4.9 / Details: Magnesium nitrate hexahydrate, Sodium citrate

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.197→36.83 Å / Num. obs: 11542 / % possible obs: 93 % / Redundancy: 12.4 % / Net I/σ(I): 17.1
Reflection shellResolution: 2.2→2.24 Å / Num. unique obs: 489

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
Cootmodel building
PHENIXphasing
MxDCdata collection
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ITC

5itc


Resolution: 2.197→36.829 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.87 / Phase error: 23.65
RfactorNum. reflection% reflection
Rfree0.2684 557 4.83 %
Rwork0.2118 --
obs0.2144 11535 93.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.197→36.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1733 0 102 52 1887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021882
X-RAY DIFFRACTIONf_angle_d0.5182545
X-RAY DIFFRACTIONf_dihedral_angle_d11.2091075
X-RAY DIFFRACTIONf_chiral_restr0.037286
X-RAY DIFFRACTIONf_plane_restr0.004298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1972-2.41830.28711130.21282446X-RAY DIFFRACTION86
2.4183-2.76810.24421240.2012674X-RAY DIFFRACTION93
2.7681-3.48710.24471610.20952776X-RAY DIFFRACTION96
3.4871-36.83420.28871590.21763082X-RAY DIFFRACTION98

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