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- PDB-3k5b: Crystal structure of the peripheral stalk of Thermus thermophilus... -

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Basic information

Entry
Database: PDB / ID: 3k5b
TitleCrystal structure of the peripheral stalk of Thermus thermophilus H+-ATPase/synthase
Components
  • V-type ATP synthase subunit E
  • V-type ATP synthase, subunit (VAPC-THERM)
KeywordsHYDROLASE / right handed coiled coil / vacuolar ATPase/synthase / V-Type ATPase/synthase / A-Type ATPase/synthase / peripheral stator / peripheral stalk / ATP synthesis / Hydrogen ion transport / Ion transport / Transport
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 / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2950 / F1F0 ATP synthase subunit B, membrane domain / ATP synthase, E subunit, C-terminal / hypothetical protein PF0899 fold / Vacuolar (H+)-ATPase G subunit / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2950 / F1F0 ATP synthase subunit B, membrane domain / ATP synthase, E subunit, C-terminal / hypothetical protein PF0899 fold / Vacuolar (H+)-ATPase G subunit / 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 / V-type ATP synthase, subunit (VAPC-THERM)
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsLee, L.K. / Stewart, A.G. / Donohoe, M. / Bernal, R.A. / Stock, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: The structure of the peripheral stalk of Thermus thermophilus H(+)-ATPase/synthase.
Authors: Lee, L.K. / Stewart, A.G. / Donohoe, M. / Bernal, R.A. / Stock, D.
History
DepositionOct 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: V-type ATP synthase, subunit (VAPC-THERM)
E: V-type ATP synthase subunit E
B: V-type ATP synthase, subunit (VAPC-THERM)
A: V-type ATP synthase subunit E


Theoretical massNumber of molelcules
Total (without water)65,1114
Polymers65,1114
Non-polymers00
Water0
1
B: V-type ATP synthase, subunit (VAPC-THERM)
A: V-type ATP synthase subunit E


Theoretical massNumber of molelcules
Total (without water)32,5562
Polymers32,5562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
Surface area18680 Å2
MethodPISA
2
G: V-type ATP synthase, subunit (VAPC-THERM)
E: V-type ATP synthase subunit E


Theoretical massNumber of molelcules
Total (without water)32,5562
Polymers32,5562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-45 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.781, 79.755, 75.796
Angle α, β, γ (deg.)90.000, 97.640, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein V-type ATP synthase, subunit (VAPC-THERM)


Mass: 11668.251 Da / Num. of mol.: 2 / Fragment: G-17: N-terminally truncated by 17 residues
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: 55981248, TTHA1279 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SIT5
#2: Protein V-type ATP synthase subunit E / V-ATPase subunit E


Mass: 20887.271 Da / Num. of mol.: 2 / Mutation: Emmm: L134M, L171M, L178M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: 55981245, atpE, TTHA1276, vatE / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P74901

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 64.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 40% MPD, 0.1 M Cacodylate pH 6.4, 5% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.97957 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 15, 2008
RadiationMonochromator: Si(111) / Protocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.536
11L, -K, H20.464
ReflectionResolution: 3.1→30 Å / Num. all: 20170 / Num. obs: 15485

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0088refinement
PDB_EXTRACT3.005data extraction
BioCARSdata collection
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 3.1→29.66 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.912 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 50.356 / SU ML: 0.397 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.288 823 5.3 %RANDOM
Rwork0.232 ---
obs0.235 15471 94.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 93.26 Å2 / Biso mean: 60.697 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-16.77 Å20 Å2-44.66 Å2
2---36.02 Å20 Å2
3---19.25 Å2
Refinement stepCycle: LAST / Resolution: 3.1→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4056 0 0 0 4056
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0214085
X-RAY DIFFRACTIONr_bond_other_d0.0010.022705
X-RAY DIFFRACTIONr_angle_refined_deg0.911.9815534
X-RAY DIFFRACTIONr_angle_other_deg0.86336572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8425563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02523.554166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.93515649
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3171547
X-RAY DIFFRACTIONr_chiral_restr0.0490.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024736
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02789
X-RAY DIFFRACTIONr_mcbond_it0.64222839
X-RAY DIFFRACTIONr_mcbond_other0.08621136
X-RAY DIFFRACTIONr_mcangle_it1.12734380
X-RAY DIFFRACTIONr_scbond_it0.58821246
X-RAY DIFFRACTIONr_scangle_it1.06131154
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 39 -
Rwork0.345 891 -
all-930 -
obs--77.44 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.19995.55243.88424.43243.14072.4763-0.41170.8524-0.0006-0.26310.5789-0.0503-0.14050.5564-0.16710.0806-0.0581-0.17760.23750.00060.594829.575416.834525.7736
21.02691.50142.18662.79884.12246.48280.08840.338-0.0630.23020.429-0.22680.38580.8537-0.51740.16580.0374-0.17960.2561-0.04070.41910.984616.75553.4359
38.40434.39734.20572.52082.22352.15750.3080.2268-0.09810.2426-0.1328-0.05930.19260.1069-0.17510.0567-0.0708-0.07570.2941-0.04050.296821.469510.732128.2564
40.6971.03542.04211.61473.13016.26380.01120.08910.01020.10940.05610.01270.24710.2851-0.06720.1691-0.022-0.08460.1843-0.01770.24857.887423.35612.2242
52.01890.0953-0.56471.77630.82120.63360.15710.31080.18020.2038-0.02530.17860.0487-0.2684-0.13180.19420.0376-0.03570.61010.13520.7799-45.8612-10.611211.1761
61.0598-0.196-0.93331.03370.3031.0224-0.4619-0.05280.04090.06410.3464-0.08510.2021-0.0880.11540.6220.0577-0.030.6658-0.01530.621415.991445.254781.9885
76.16410.0066-0.36330.05630.27672.4322-0.13-0.3384-0.45690.0347-0.01160.10730.0716-0.05940.14170.15110.0040.03160.097-0.03540.4866-22.6162-11.6416.8771
86.52041.6253-3.47731.24910.8885.54940.17050.26830.50710.014-0.04530.264-0.2957-0.3062-0.12520.4185-0.02410.02460.16730.03580.583213.023145.800357.6
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1G1 - 110
2X-RAY DIFFRACTION2B1 - 110
3X-RAY DIFFRACTION3E1 - 95
4X-RAY DIFFRACTION4A1 - 95
5X-RAY DIFFRACTION5E96 - 166
6X-RAY DIFFRACTION6A96 - 166
7X-RAY DIFFRACTION7E167 - 187
8X-RAY DIFFRACTION8A167 - 187

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