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- PDB-1aqt: EPSILON SUBUNIT OF F1F0-ATP SYNTHASE FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1aqt
TitleEPSILON SUBUNIT OF F1F0-ATP SYNTHASE FROM ESCHERICHIA COLI
ComponentsATP SYNTHASE
KeywordsHYDROLASE / ATPASE / ATP SYNTHASE / EPSILON SUBUNIT
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 ATP synthase activity, rotational mechanism / ATP binding / 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 delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix 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 delta/epsilon subunit, C-terminal domain / ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ATP synthase epsilon chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.3 Å
AuthorsUhlin, U. / Guss, J.M.
Citation
Journal: Structure / Year: 1997
Title: Crystal structure of the epsilon subunit of the proton-translocating ATP synthase from Escherichia coli.
Authors: Uhlin, U. / Cox, G.B. / Guss, J.M.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: The Expression, Purification and Crystallization of the Epsilon Subunit of the F1 Portion of the ATPase of Escherichia Coli
Authors: Codd, R. / Cox, G.B. / Guss, J.M. / Solomon, R.G. / Webb, D.
History
DepositionJul 31, 1997Processing site: BNL
Revision 1.0Feb 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP SYNTHASE


Theoretical massNumber of molelcules
Total (without water)14,8981
Polymers14,8981
Non-polymers00
Water25214
1
A: ATP SYNTHASE

A: ATP SYNTHASE


Theoretical massNumber of molelcules
Total (without water)29,7962
Polymers29,7962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_556-x+y,y,-z+3/21
Unit cell
Length a, b, c (Å)94.610, 94.610, 56.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein ATP SYNTHASE


Mass: 14897.904 Da / Num. of mol.: 1 / Fragment: EPSILON CHAIN / Mutation: A1G, M2S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: AN2994 / Plasmid: PAN590 / Gene (production host): UNCC / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6E6, EC: 3.6.1.34
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.4 Å3/Da / Density % sol: 50 %
Crystal growpH: 7.5
Details: PROTEIN (4 MG/ML)IN 50 MM HEPES BUFFER, PH 7.5, 200 MM (NH2)2SO4, 2 M (NA/K)PO4
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 M1reservoirK2HPO4/NaH2PO4/H2O
2100 mMHEPES1reservoir
3200 mM1reservoirNH2SO4
42 mg/mlprotein1drop
51 M1dropK2HPO4/NaH2PO4/H2O
650 mMHEPES1drop
7100 mM1dropNH2SO4

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 1, 1994 / Details: MIRRORS
RadiationMonochromator: NI FILTER (0.00015") / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→19 Å / Num. obs: 6626 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 31 Å2 / Rsym value: 0.059 / Net I/σ(I): 12.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.48 / % possible all: 89
Reflection
*PLUS
Num. measured all: 19833 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 89 % / Rmerge(I) obs: 0.475

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Processing

Software
NameVersionClassification
X-PLOR3.843model building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.843phasing
RefinementMethod to determine structure: MIR / Resolution: 2.3→19 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.288 511 8 %RANDOM
Rwork0.214 ---
obs0.214 6134 87 %-
Displacement parametersBiso mean: 41 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1027 0 0 14 1041
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.81.5
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it5.22
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.533 46 7.9 %
Rwork0.453 583 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX_TIP3.PROTOPHCSDX_TIP3.PRO
X-RAY DIFFRACTION2

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