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- PDB-5zwl: Crystal structure of the gamma - epsilon complex of photosyntheti... -

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Basic information

Entry
Database: PDB / ID: 5zwl
TitleCrystal structure of the gamma - epsilon complex of photosynthetic cyanobacterial F1-ATPase
Components
  • ATP synthase epsilon chain
  • ATP synthase gamma chain
KeywordsHYDROLASE / ATP synthase gamma epsilon cyanobacteria redox regulation
Function / homology
Function and homology information


plasma membrane-derived thylakoid membrane / proton-transporting ATP synthase complex, catalytic core F(1) / proton-transporting ATP synthase activity, rotational mechanism / ATP binding
Similarity search - Function
ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / Helix hairpin bin / ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F1 complex, gamma subunit conserved site ...ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / Helix hairpin bin / ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / Helix Hairpins / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ATP synthase epsilon chain / ATP synthase gamma chain
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.98 Å
AuthorsMurakami, S. / Yamashita, E. / Hisabori, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP18am0101072 Japan
CitationJournal: Biochem. J. / Year: 2018
Title: Structure of the gamma-epsilon complex of cyanobacterial F1-ATPase reveals a suppression mechanism of the gamma subunit on ATP hydrolysis in phototrophs.
Authors: Murakami, S. / Kondo, K. / Katayama, S. / Hara, S. / Sunamura, E.I. / Yamashita, E. / Groth, G. / Hisabori, T.
History
DepositionMay 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
E: ATP synthase epsilon chain
G: ATP synthase gamma chain


Theoretical massNumber of molelcules
Total (without water)45,8662
Polymers45,8662
Non-polymers00
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-17 kcal/mol
Surface area18210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.556, 71.556, 204.969
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein ATP synthase epsilon chain / Epsilon subunit of F1-ATPase / ATP synthase F1 sector epsilon subunit / F-ATPase epsilon subunit


Mass: 14764.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / Gene: atpC, atpE, tlr0526 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8DLG7
#2: Protein ATP synthase gamma chain / Gamma subunit of F1-ATPase / ATP synthase F1 sector gamma subunit / F-ATPase gamma subunit


Mass: 31100.865 Da / Num. of mol.: 1 / Mutation: R33A,R34A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / Gene: atpG, atpC, tll0385 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8DLU1
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 3.06 Å3/Da / Density % sol: 59.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: sodium/potassium phosphate buffer (pH 6.0), sodium chloride, PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.98→36.004 Å / Num. obs: 37645 / % possible obs: 98.5 % / Redundancy: 6.8 % / CC1/2: 0.861 / Rmerge(I) obs: 0.055 / Net I/σ(I): 38.1
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 5 % / Rmerge(I) obs: 0.866 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1666 / % possible all: 89.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.98→36.004 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.78
RfactorNum. reflection% reflection
Rfree0.242 1814 4.87 %
Rwork0.2051 --
obs0.2069 37282 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.98→36.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3012 0 0 178 3190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123057
X-RAY DIFFRACTIONf_angle_d1.2444148
X-RAY DIFFRACTIONf_dihedral_angle_d6.0962381
X-RAY DIFFRACTIONf_chiral_restr0.069498
X-RAY DIFFRACTIONf_plane_restr0.007542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9799-2.03350.40651190.37412448X-RAY DIFFRACTION89
2.0335-2.09330.37091470.31942578X-RAY DIFFRACTION95
2.0933-2.16090.29241320.29162682X-RAY DIFFRACTION98
2.1609-2.23810.29781320.25262727X-RAY DIFFRACTION99
2.2381-2.32770.30061320.23822684X-RAY DIFFRACTION99
2.3277-2.43360.26651410.2132734X-RAY DIFFRACTION99
2.4336-2.56190.27241350.22682738X-RAY DIFFRACTION99
2.5619-2.72230.29751560.22012724X-RAY DIFFRACTION99
2.7223-2.93240.25891300.22992778X-RAY DIFFRACTION100
2.9324-3.22740.30441540.21692780X-RAY DIFFRACTION100
3.2274-3.6940.23731450.20222804X-RAY DIFFRACTION100
3.694-4.65240.20781360.17062886X-RAY DIFFRACTION100
4.6524-36.00960.20171550.18982905X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 0.3973 Å / Origin y: 31.2725 Å / Origin z: -26.0188 Å
111213212223313233
T0.6944 Å20.0406 Å2-0.0188 Å2-0.4063 Å20.0122 Å2--0.3757 Å2
L1.8572 °20.4661 °21.8983 °2-0.7028 °20.6922 °2--4.5118 °2
S-0.0201 Å °-0.008 Å °0.292 Å °0.1022 Å °-0.164 Å °0.0939 Å °-0.4133 Å °-0.1102 Å °0.1467 Å °
Refinement TLS groupSelection details: all

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