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- PDB-4dt0: The structure of the peripheral stalk subunit E from Pyrococcus h... -

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Basic information

Entry
Database: PDB / ID: 4dt0
TitleThe structure of the peripheral stalk subunit E from Pyrococcus horikoshii
ComponentsV-type ATP synthase subunit E
KeywordsHYDROLASE / A-ATP synthase / peripheral stalk
Function / homology
Function and homology information


proton-transporting two-sector ATPase complex, catalytic domain / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP binding
Similarity search - Function
F1F0 ATP synthase subunit B, membrane domain / ATP synthase, E subunit, C-terminal / hypothetical protein PF0899 fold / F-type ATP synthase subunit B-like, membrane domain superfamily / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / 2-Layer Sandwich ...F1F0 ATP synthase subunit B, membrane domain / ATP synthase, E subunit, C-terminal / hypothetical protein PF0899 fold / F-type ATP synthase subunit B-like, membrane domain superfamily / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
V-type ATP synthase subunit E
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.65 Å
AuthorsBalakrishna, A.M. / Gruber, G.
Citation
Journal: J.Mol.Biol. / Year: 2012
Title: The structure of subunit E of the Pyrococcus horikoshii OT3 A-ATP synthase gives insight into the elasticity of the peripheral stalk.
Authors: Balakrishna, A.M. / Hunke, C. / Gruber, G.
#1: Journal: J.Mol.Biol. / Year: 2007
Title: Dimeric core structure of modular stator subunit E of archaeal H+ -ATPase.
Authors: Lokanath, N.K. / Matsuura, Y. / Kuroishi, C. / Takahashi, N. / Kunishima, N.
History
DepositionFeb 20, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 20, 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
A: V-type ATP synthase subunit E


Theoretical massNumber of molelcules
Total (without water)24,1831
Polymers24,1831
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.828, 111.828, 95.466
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein V-type ATP synthase subunit E / V-ATPase subunit E


Mass: 24182.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: atpE, PH1978 / Plasmid: pET22b(+)-His6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIL / References: UniProt: O57724

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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: 3.25 Å3/Da / Density % sol: 62.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10% 2-propanol, 100mM 2-morpholinoethanesulfonic acid, sodium salt (pH 6.0), 200mM calcium acetate, 0.01 M potassium sodium tartrate tetrahydrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.979, 0.978, 0.963
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 24, 2011
Details: Vertically Collimating Premirror, Toroidal Focusing Mirror
RadiationMonochromator: Double Crystal Si(111) Monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.9781
30.9631
ReflectionResolution: 3.65→30 Å / Num. all: 3599 / Num. obs: 3564 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 88.63 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.5
Reflection shellResolution: 3.65→3.78 Å / Redundancy: 4 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.08 / Num. unique all: 3599 / % possible all: 99.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 3.65→26.85 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.861 / SU B: 128.307 / SU ML: 0.898 / Cross valid method: THROUGHOUT / ESU R Free: 0.748 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.35669 257 8.2 %RANDOM
Rwork0.32312 ---
obs0.32593 2879 100 %-
all-3136 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.928 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 3.65→26.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms898 0 0 0 898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02897
X-RAY DIFFRACTIONr_angle_refined_deg1.0641.9361250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5765180
X-RAY DIFFRACTIONr_chiral_restr0.0550.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02724
X-RAY DIFFRACTIONr_mcbond_it0.3461.5897
X-RAY DIFFRACTIONr_mcangle_it0.64521250
LS refinement shellResolution: 3.651→3.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 13 -
Rwork0.32 172 -
obs-172 100 %
Refinement TLS params.Method: refined / Origin x: 11.0024 Å / Origin y: -9.924 Å / Origin z: 0.3318 Å
111213212223313233
T0.178 Å20.0011 Å2-0.0075 Å2-0.1071 Å2-0.0628 Å2--0.2652 Å2
L7.2929 °21.3294 °24.2547 °2-0.5545 °20.4777 °2--2.8423 °2
S-0.0405 Å °-0.2135 Å °-0.2706 Å °0.1121 Å °-0.0603 Å °-0.2187 Å °-0.1382 Å °-0.1232 Å °0.1008 Å °

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