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- PDB-1fs0: COMPLEX OF GAMMA/EPSILON ATP SYNTHASE FROM E.COLI -

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Basic information

Entry
Database: PDB / ID: 1fs0
TitleCOMPLEX OF GAMMA/EPSILON ATP SYNTHASE FROM E.COLI
Components
  • ATP SYNTHASE EPSILON SUBUNIT
  • ATP SYNTHASE GAMMA SUBUNIT
KeywordsHYDROLASE / ATP Synthase / Coiled coil / Gamma / epsilon
Function / homology
Function and homology information


proton-transporting ATP synthase complex / proton motive force-driven plasma membrane ATP synthesis / proton motive force-driven ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP binding / membrane / plasma membrane
Similarity search - Function
ATP synthase delta/epsilon subunit, C-terminal domain / ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / Pyruvate Kinase; Chain: A, domain 1 / ATP synthase, gamma subunit, helix hairpin domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F1 complex, delta/epsilon subunit ...ATP synthase delta/epsilon subunit, C-terminal domain / ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / Pyruvate Kinase; Chain: A, domain 1 / ATP synthase, gamma subunit, helix hairpin domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Up-down Bundle / Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ATP synthase epsilon chain / ATP synthase gamma chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsWilce, M.C.J. / Rodgers, A.J.W.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Structure of the gamma-epsilon complex of ATP synthase.
Authors: Rodgers, A.J. / Wilce, M.C.
History
DepositionSep 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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 SUBUNIT
G: ATP SYNTHASE GAMMA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)40,6402
Polymers40,6402
Non-polymers00
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-26 kcal/mol
Surface area16530 Å2
MethodPISA
2
E: ATP SYNTHASE EPSILON SUBUNIT
G: ATP SYNTHASE GAMMA SUBUNIT

E: ATP SYNTHASE EPSILON SUBUNIT
G: ATP SYNTHASE GAMMA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)81,2804
Polymers81,2804
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
Buried area11130 Å2
ΔGint-62 kcal/mol
Surface area30240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.720, 176.090, 67.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein ATP SYNTHASE EPSILON SUBUNIT


Mass: 14956.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A6E6, EC: 3.6.1.34
#2: Protein ATP SYNTHASE GAMMA SUBUNIT /


Mass: 25683.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ABA6, EC: 3.6.1.34
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 0.5M tartrate, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.5 Mtartrate1reservoir
20.1 MTris-HCl1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
41
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)Wavelength
SYNCHROTRONAPS 14-BM-C10.9795, 0.9793, 0.9537
ROTATING ANODERIGAKU RU20041.54181.5418
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDApr 17, 2000
MAR scanner 345 mm plate4IMAGE PLATEFeb 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97931
30.95371
41.54181
ReflectionResolution: 2.02→20 Å / Num. all: 26978 / Num. obs: 26978 / % possible obs: 89.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 35.2 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 20
Reflection shellResolution: 2.02→2.15 Å / Redundancy: 5 % / Rmerge(I) obs: 0.256 / Num. unique all: 2744 / % possible all: 63.2
Reflection shell
*PLUS
% possible obs: 63.2 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.1→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: engh and huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1224 -random 5%
Rwork0.216 ---
all0.227 26 --
obs0.227 25543 10 %-
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2691 0 0 254 2945
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.65
X-RAY DIFFRACTIONc_bond_d0.085

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