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- PDB-6a7k: X-ray structure of NdhS from T. elongatus -

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Entry
Database: PDB / ID: 6a7k
TitleX-ray structure of NdhS from T. elongatus
ComponentsTlr0636 protein
KeywordsELECTRON TRANSPORT / NADH dehydrogenase-like complex / NDH-1 / cyclic electron flow (CEF) / Ferredoxin
Function / homologyNAD(P)H dehydrogenase subunit S / NADH dehydrogenase-like complex, subunit S / photosynthetic electron transport chain / Tlr0636 protein
Function and homology information
Specimen sourceThermosynechococcus elongatus (Cyanobacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.9 Å resolution
AuthorsUmeno, K. / Misumi, Y. / Tanaka, H. / Kurisu, G.
CitationJournal: Science / Year: 2019
Title: Structural adaptations of photosynthetic complex I enable ferredoxin-dependent electron transfer.
Authors: Jan M Schuller / James A Birrell / Hideaki Tanaka / Tsuyoshi Konuma / Hannes Wulfhorst / Nicholas Cox / Sandra K Schuller / Jacqueline Thiemann / Wolfgang Lubitz / Pierre Sétif / Takahisa Ikegami / Benjamin D Engel / Genji Kurisu / Marc M Nowaczyk
Abstract: Photosynthetic complex I enables cyclic electron flow around photosystem I, a regulatory mechanism for photosynthetic energy conversion. We report a 3.3-angstrom-resolution cryo-electron microscopy ...Photosynthetic complex I enables cyclic electron flow around photosystem I, a regulatory mechanism for photosynthetic energy conversion. We report a 3.3-angstrom-resolution cryo-electron microscopy structure of photosynthetic complex I from the cyanobacterium The model reveals structural adaptations that facilitate binding and electron transfer from the photosynthetic electron carrier ferredoxin. By mimicking cyclic electron flow with isolated components in vitro, we demonstrate that ferredoxin directly mediates electron transfer between photosystem I and complex I, instead of using intermediates such as NADPH (the reduced form of nicotinamide adenine dinucleotide phosphate). A large rate constant for association of ferredoxin to complex I indicates efficient recognition, with the protein subunit NdhS being the key component in this process.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 3, 2018 / Release: Jan 16, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 16, 2019Structure modelrepositoryInitial release
1.1Jan 30, 2019Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tlr0636 protein
B: Tlr0636 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5674
Polyers16,4472
Non-polymers1202
Water1,910106
1
A: Tlr0636 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2842
Polyers8,2241
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tlr0636 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2842
Polyers8,2241
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)1370
ΔGint (kcal/M)-0
Surface area (Å2)7630
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)58.850, 58.850, 225.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP 65 2 2

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Components

#1: Protein/peptide Tlr0636 protein / NdhS


Mass: 8223.556 Da / Num. of mol.: 2
Source: (gene. exp.) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Strain: BP-1 / Gene: tlr0636 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DL61
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Formula: C2H4O2 / Acetic acid
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Formula: H2O / Water

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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: 3.4 / Density percent sol: 64.2 %
Crystal growTemp: 293 K / Method: vapor diffusion, hanging drop
Details: 100mM Sodium acetate trihydrate (pH 4.6), 100mM CdCl2, 38 % (v/v) polyethylene glycol (PEG) 400

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: SPRING-8 BEAMLINE BL44XU / Synchrotron site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9
DetectorType: RAYONIX MX300HE / Detector: CCD / Collection date: Nov 14, 2017
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionD resolution high: 1.9 Å / D resolution low: 49.71 Å / Number obs: 19195 / CC half: 1 / Rmerge I obs: 0.058 / NetI over sigmaI: 29 / Redundancy: 11.6 % / Percent possible obs: 100
Reflection shellRmerge I obs: 0.399 / Highest resolution: 1.9 Å / Lowest resolution: 1.94 Å / MeanI over sigI obs: 8.25 / Number unique obs: 2520 / CC half: 0.985 / Redundancy: 11.6 % / Percent possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSVERSION Jan 26, 2018data reduction
XDSVERSION Jan 26, 2018data scaling
PHASER2.8.2phasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C4S
Correlation coeff Fo to Fc: 0.933 / Correlation coeff Fo to Fc free: 0.931 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / Overall SU B: 1.858 / Overall SU ML: 0.057 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Overall ESU R: 0.025 / Overall ESU R Free: 0.024
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å
Displacement parametersB iso mean: 28.596 Å2 / Aniso B11: 8.77 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 8.77 Å2 / Aniso B23: 0 Å2 / Aniso B33: -17.55 Å2
Least-squares processR factor R free: 0.23783 / R factor R work: 0.21858 / R factor obs: 0.21957 / Highest resolution: 1.9 Å / Lowest resolution: 49.71 Å / Number reflection R free: 960 / Number reflection obs: 18235 / Percent reflection R free: 5 / Percent reflection obs: 99.95
Refine hist #1Highest resolution: 1.9 Å / Lowest resolution: 49.71 Å
Number of atoms included #1Protein: 948 / Nucleic acid: 0 / Ligand: 8 / Solvent: 106 / Total: 1062
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.020981
X-RAY DIFFRACTIONr_bond_other_d0.0020.020923
X-RAY DIFFRACTIONr_angle_refined_deg2.1091.9651335
X-RAY DIFFRACTIONr_angle_other_deg1.0783.0002144
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3815.000121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg47.19226.19042
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19015.000166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.35915.0002
X-RAY DIFFRACTIONr_chiral_restr0.1680.200158
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211077
X-RAY DIFFRACTIONr_gen_planes_other0.0010.020181
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2062.484489
X-RAY DIFFRACTIONr_mcbond_other3.0532.473486
X-RAY DIFFRACTIONr_mcangle_it4.4153.679607
X-RAY DIFFRACTIONr_mcangle_other4.4283.683608
X-RAY DIFFRACTIONr_scbond_it4.9302.966492
X-RAY DIFFRACTIONr_scbond_other4.9252.970493
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9294.288729
X-RAY DIFFRACTIONr_long_range_B_refined9.98732.2171003
X-RAY DIFFRACTIONr_long_range_B_other9.98432.2591004
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints ncs

Ens ID: 1 / Number: 2968 / Refine ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom IDAuth asym ID
1A
2B
Refine LS shellHighest resolution: 1.9 Å / R factor R free: 0.213 / R factor R work: 0.19 / Lowest resolution: 1.949 Å / Number reflection R free: 68 / Number reflection R work: 1289 / Total number of bins used: 20 / Percent reflection obs: 1

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