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- PDB-2d00: Subunit F of V-type ATPase/synthase -

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Basic information

Entry
Database: PDB / ID: 2d00
TitleSubunit F of V-type ATPase/synthase
ComponentsV-type ATP synthase subunit F
KeywordsHYDROLASE / V-ATPase / Subunit F / CheY / FRET
Function / homology
Function and homology information


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
Helix Hairpins - #810 / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F, bacterial/archaeal / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase (F/14-kDa) subunit / Helix Hairpins / Helix non-globular / Special / Rossmann fold ...Helix Hairpins - #810 / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F, bacterial/archaeal / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase (F/14-kDa) subunit / Helix Hairpins / Helix non-globular / Special / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
V-type ATP synthase subunit F
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsMakyio, H. / Iino, R. / Ikeda, C. / Imamura, H. / Tamakoshi, M. / Iwata, M. / Stock, D. / Bernal, R.A. / Carpenter, E.P. / Yoshida, M. ...Makyio, H. / Iino, R. / Ikeda, C. / Imamura, H. / Tamakoshi, M. / Iwata, M. / Stock, D. / Bernal, R.A. / Carpenter, E.P. / Yoshida, M. / Yokoyama, K. / Iwata, S.
CitationJournal: Embo J. / Year: 2005
Title: Structure of a central stalk subunit F of prokaryotic V-type ATPase/synthase from Thermus thermophilus
Authors: Makyio, H. / Iino, R. / Ikeda, C. / Imamura, H. / Tamakoshi, M. / Iwata, M. / Stock, D. / Bernal, R.A. / Carpenter, E.P. / Yoshida, M. / Yokoyama, K. / Iwata, S.
History
DepositionJul 21, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: V-type ATP synthase subunit F
B: V-type ATP synthase subunit F
C: V-type ATP synthase subunit F
D: V-type ATP synthase subunit F
E: V-type ATP synthase subunit F
F: V-type ATP synthase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,43210
Polymers71,2726
Non-polymers1604
Water5,170287
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: V-type ATP synthase subunit F
B: V-type ATP synthase subunit F
C: V-type ATP synthase subunit F
D: V-type ATP synthase subunit F
E: V-type ATP synthase subunit F
F: V-type ATP synthase subunit F
hetero molecules

A: V-type ATP synthase subunit F
B: V-type ATP synthase subunit F
C: V-type ATP synthase subunit F
D: V-type ATP synthase subunit F
E: V-type ATP synthase subunit F
F: V-type ATP synthase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,86520
Polymers142,54412
Non-polymers3218
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area48090 Å2
ΔGint-491 kcal/mol
Surface area55510 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)81.705, 138.295, 66.096
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 11878.670 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P74903, H+-transporting two-sector ATPase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.59 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 400, calcium acetate, potassium chloride, MES, MOPS, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA10.979
SYNCHROTRONESRF ID14-420.9794, 0.9796, 0.9724
Detector
TypeIDDetectorDate
MARRESEARCH1CCDNov 3, 2003
ADSC QUANTUM 42CCDNov 13, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97941
30.97961
40.97241
ReflectionResolution: 2.2→26 Å / Num. all: 38602 / Num. obs: 38602 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.28 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→25 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.922 / SU B: 16.474 / SU ML: 0.214 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26221 1206 3.1 %RANDOM
Rwork0.21403 ---
obs-37320 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 64.158 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å20 Å2
2---0.99 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4998 0 4 287 5289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0225070
X-RAY DIFFRACTIONr_bond_other_d0.0060.024950
X-RAY DIFFRACTIONr_angle_refined_deg2.4922.0156852
X-RAY DIFFRACTIONr_angle_other_deg1.109311418
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7795648
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.6723.243222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.54715888
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2061554
X-RAY DIFFRACTIONr_chiral_restr0.1480.2780
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025676
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021002
X-RAY DIFFRACTIONr_nbd_refined0.2730.21317
X-RAY DIFFRACTIONr_nbd_other0.2220.25449
X-RAY DIFFRACTIONr_nbtor_refined0.1960.22421
X-RAY DIFFRACTIONr_nbtor_other0.1030.23461
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2710.2288
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.3730.24
X-RAY DIFFRACTIONr_metal_ion_refined0.1340.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.244
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2110.2136
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3140.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0240.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4581.53414
X-RAY DIFFRACTIONr_mcbond_other0.3871.51350
X-RAY DIFFRACTIONr_mcangle_it2.06525160
X-RAY DIFFRACTIONr_scbond_it3.41231928
X-RAY DIFFRACTIONr_scangle_it5.3134.51692
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 72 -
Rwork0.261 2711 -
obs--100 %
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)
19.85510.2049-0.253515.25443.02145.3566-0.43110.05940.3677-1.51060.6334-0.8316-0.2840.3167-0.2023-0.0784-0.16150.0116-0.16680.0795-0.292334.724641.01718.7566
28.94964.1125-5.73147.7416-2.606713.8086-0.26511.3419-0.2092-1.40530.18290.0716-0.3375-0.67610.0822-0.05030.012-0.0362-0.1337-0.1116-0.175355.63745.6682-24.0891
30.72930.05252.248710.10951.14327.4883-0.1640.3996-0.1222-0.03680.18060.03640.69550.2281-0.0165-0.0756-0.04460.2266-0.1044-0.0840.202914.276261.19278.3463
411.0476-2.7379-7.92796.03544.066614.73130.03411.4215-0.0777-0.93460.13680.3056-0.68090.3117-0.1709-0.19-0.1377-0.0845-0.0022-0.0199-0.16228.253343.9442-24.1484
516.0994-2.35286.19166.3341-3.26747.76961.43471.1647-1.4455-1.0093-0.80630.41210.98570.6004-0.62840.02830.254-0.0712-0.1275-0.125-0.216720.391888.2498.6715
63.4543-0.3851.011414.62037.332911.94820.27321.0579-0.1579-1.93830.08330.5824-0.07990.987-0.3565-0.02510.0444-0.12440.04480.0496-0.027514.703367.7356-24.6669
710.2665-0.351-3.13333.0944-0.39559.01370.07860.19240.01540.5833-0.12780.2799-0.7201-0.08420.0492-0.2715-0.06410.0156-0.3788-0.0209-0.298730.455343.6855-12.7206
810.5557-0.47-0.34275.5133-2.024413.6937-0.0297-1.1139-0.23291.37440.679-0.0903-0.09910.6006-0.64930.2218-0.06560.10760.1145-0.07630.230715.705358.637819.4215
94.3027-4.9657-1.976310.87754.17716.3277-0.1573-0.0688-0.02030.4149-0.070.63780.09830.14870.2273-0.3105-0.0152-0.0454-0.31990.0241-0.056814.925365.6178-13.4394
106.35471.95553.418410.27963.042512.49460.2056-0.5366-0.63221.4209-0.00470.75410.8370.7921-0.20090.04340.0770.03530.02890.0793-0.065219.143885.831320.0536
115.9013.0196-2.42198.4197-2.92998.0135-0.3561-0.2312-0.1838-0.01010.22550.1080.1097-0.38410.1305-0.43180.00730.0148-0.3435-0.0196-0.364956.982347.2672-12.7944
1213.09232.873-1.48246.3826-1.82878.45070.48-1.77080.08870.8603-0.2016-0.5853-0.4870.4331-0.27840.20910.0252-0.03540.2435-0.0224-0.133936.944741.588320.0638
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 691 - 69
2X-RAY DIFFRACTION2AA70 - 10970 - 109
3X-RAY DIFFRACTION3BB1 - 691 - 69
4X-RAY DIFFRACTION4BB70 - 10970 - 109
5X-RAY DIFFRACTION5CC1 - 691 - 69
6X-RAY DIFFRACTION6CC70 - 10970 - 109
7X-RAY DIFFRACTION7DD1 - 691 - 69
8X-RAY DIFFRACTION8DD70 - 10970 - 109
9X-RAY DIFFRACTION9EE1 - 691 - 69
10X-RAY DIFFRACTION10EE70 - 10970 - 109
11X-RAY DIFFRACTION11FF1 - 691 - 69
12X-RAY DIFFRACTION12FF70 - 10970 - 109

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