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- PDB-3nd9: Structural characterization for the nucleotide binding ability of... -

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Basic information

Entry
Database: PDB / ID: 3nd9
TitleStructural characterization for the nucleotide binding ability of subunit A of the A1AO ATP synthase
ComponentsV-type ATP synthase alpha chain
KeywordsHYDROLASE
Function / homology
Function and homology information


intron homing / intein-mediated protein splicing / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase activity, rotational mechanism / endonuclease activity / Hydrolases; Acting on ester bonds / ATP binding / plasma membrane
Similarity search - Function
Intein splicing domain / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region ...Intein splicing domain / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Homing endonuclease / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit barrel-sandwich domain / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
A-type ATP synthase subunit A
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKumar, A. / Jeyakanthan, J. / Gruber, G.
Citation
Journal: J.Mol.Biol. / Year: 2011
Title: The transition-like state and Pi entrance into the catalytic a subunit of the biological engine A-ATP synthase.
Authors: Manimekalai, M.S. / Kumar, A. / Jeyakanthan, J. / Gruber, G.
#1: Journal: J.Mol.Biol. / Year: 2010
Title: Nucleotide Binding States of Subunit A of the A-ATP Synthase and the Implication of P-Loop Switch in Evolution.
Authors: Kumar, A. / Manimekalai, S.M.S. / Balakrishna, A.M. / Jeyakanthan, J. / Gruber, G.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Structure of the catalytic nucleotide-binding subunit A of A-type ATP synthase from Pyrococcus horikoshii reveals a novel domain related to the peripheral stalk.
Authors: Maegawa, Y. / Morita, H. / Iyaguchi, D. / Yao, M. / Watanabe, N. / Tanaka, I.
History
DepositionJun 7, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 11, 2013Group: Database references
Revision 1.3Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Nov 1, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9823
Polymers65,7461
Non-polymers2362
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.381, 128.381, 105.057
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-617-

HOH

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Components

#1: Protein V-type ATP synthase alpha chain / A-TYPE ATP SYNTHASE CATALYTIC SUBUNIT A / V-ATPase subunit A


Mass: 65745.781 Da / Num. of mol.: 1 / Fragment: catalytic (UNP residues 1-240, 617-964) / Mutation: T241A, G79R
Source method: isolated from a genetically manipulated source
Details: THE FUSION OF RESIDUES 1-240 AND RESIDUES 617-964 from V-ATPase subunit A
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET22b(+)-His6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIL
References: UniProt: O57728, H+-transporting two-sector ATPase
#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.29 Å3/Da / Density % sol: 62.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 50% (v/v) MPD, 0.1 M acetate (pH 4.5), vapor diffusion, hanging drop , temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 18, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 3.1 Å / Num. all: 16296 / Num. obs: 16262

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VDZ

1vdz


Resolution: 3.1→29.9 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.863 / SU B: 37.313 / SU ML: 0.316 / Cross valid method: THROUGHOUT / ESU R Free: 0.458 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28531 834 5.1 %RANDOM
Rwork0.21981 ---
obs0.22303 15631 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 3.1→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4004 0 16 27 4047
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224105
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.9815559
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3825506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30723.616177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.53815728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1911533
X-RAY DIFFRACTIONr_chiral_restr0.1140.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213073
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7791.52531
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.47424101
X-RAY DIFFRACTIONr_scbond_it1.78931574
X-RAY DIFFRACTIONr_scangle_it3.2394.51458
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 67 -
Rwork0.214 1126 -
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)
11.7-0.8153-0.69282.25750.24891.1721-0.2305-0.24670.15940.49040.2835-0.0337-0.0287-0.0505-0.0530.21150.1747-0.03790.1676-0.04750.02424.518943.683430.1882
21.0096-0.9501-0.10521.75140.59470.5146-0.1803-0.2537-0.04810.2330.2586-0.02420.0932-0.062-0.07830.12470.0846-0.010.18720.00140.04336.133925.064623.6326
31.7694-1.70370.71691.8964-0.52041.7014-0.1701-0.1754-0.12130.32320.27140.20750.1136-0.2289-0.10130.14640.1150.03360.18410.01870.077725.915126.199224.9561
40.6744-0.5373-0.20211.67090.20160.9589-0.05570.0192-0.13420.0487-0.02110.16030.1215-0.17970.07690.0518-0.02320.00620.1176-0.01420.09339.79797.577310.9469
51.0498-0.4268-0.46671.83121.31291.7916-0.0319-0.02340.0194-0.1120.1552-0.2288-0.07590.1346-0.12330.0523-0.0210.00170.0776-0.01650.135358.614911.04843.091
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A63 - 188
2X-RAY DIFFRACTION2A189 - 288
3X-RAY DIFFRACTION3A289 - 388
4X-RAY DIFFRACTION4A389 - 488
5X-RAY DIFFRACTION5A489 - 588

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