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- PDB-2e5y: Epsilon subunit and ATP complex of F1F0-ATP synthase from the The... -

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Basic information

Entry
Database: PDB / ID: 2e5y
TitleEpsilon subunit and ATP complex of F1F0-ATP synthase from the Thermophilic Bacillus PS3
ComponentsATP synthase epsilon chain
KeywordsHYDROLASE / ATP synthase / F1FO ATP synthase / F1-ATPase / Epsilon subunit / ATP
Function / homology
Function and homology information


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
ADENOSINE-5'-TRIPHOSPHATE / ATP synthase epsilon chain
Similarity search - Component
Biological speciesBacillus sp. PS3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsYagi, H. / Akutsu, H.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structures of the thermophilic F1-ATPase {varepsilon} subunit suggesting ATP-regulated arm motion of its C-terminal domain in F1
Authors: Yagi, H. / Kajiwara, N. / Tanaka, H. / Tsukihara, T. / Kato-Yamada, Y. / Yoshida, M. / Akutsu, H.
History
DepositionDec 25, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The 74th residues is LYS and 96th-103th residues are AKERAERR instead of RKSGRTP according ...SEQUENCE The 74th residues is LYS and 96th-103th residues are AKERAERR instead of RKSGRTP according to Kato-Yamada Y., Yoshida M., Hisabori T. [J.Biol.Chem. 275:35746-35750(2000).].

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP synthase epsilon chain
B: ATP synthase epsilon chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1864
Polymers29,1722
Non-polymers1,0142
Water3,693205
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.480, 64.917, 103.944
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ATP synthase epsilon chain / ATP synthase F1 sector epsilon subunit


Mass: 14585.905 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Plasmid: pet32a / Production host: Escherichia coli (E. coli)
References: UniProt: P07678, H+-transporting two-sector ATPase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 5% PEG 6000, 0.1M citric acid, pH 4.0, Vapor diffusion, hanging drop, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Apr 18, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.92→10 Å / Num. obs: 17451 / % possible obs: 92.5 % / Biso Wilson estimate: 27.95 Å2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AQT

1aqt


Resolution: 1.92→10 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.903 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.182
RfactorNum. reflection% reflectionSelection details
Rfree0.25 948 5.2 %RANDOM
Rwork0.2 ---
obs0.20211 17451 92.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.821 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2--1.74 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 1.92→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 62 205 2309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222130
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2082.0352880
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0645264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05923.8184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.79915404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6761520
X-RAY DIFFRACTIONr_chiral_restr0.30.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021546
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.2931
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21427
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2200
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0840.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2861.51369
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.06122130
X-RAY DIFFRACTIONr_scbond_it2.9443837
X-RAY DIFFRACTIONr_scangle_it4.5994.5750
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.968 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 47 -
Rwork0.199 841 -
obs--62.45 %

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