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- PDB-3mfy: Structural characterization of the subunit A mutant F236A of the ... -

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Basic information

Entry
Database: PDB / ID: 3mfy
TitleStructural characterization of the subunit A mutant F236A of the A-ATP synthase from Pyrococcus horikoshii
ComponentsV-type ATP synthase alpha chain
KeywordsHYDROLASE / A-Type ATP synthase / P loop / Phenylalanine mutant
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
ACETIC ACID / A-type ATP synthase subunit A
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBalakrishna, A.M. / Kumar, A. / Manimekali, M.S.S. / Jeyakanthan, J. / Gruber, G.
Citation
Journal: J.Mol.Biol. / Year: 2010
Title: The critical roles of residues P235 and F236 of subunit A of the motor protein A-ATP synthase in P-loop formation and nucleotide binding.
Authors: Kumar, A. / Manimekalai, M.S. / Balakrishna, A.M. / Priya, R. / Biukovic, G. / Jeyakanthan, J. / Gruber, G.
#1: Journal: J.Mol.Biol. / Year: 2009
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, M.S.S. / Balakrishna, A.M. / Jeyakanthan, J. / Gerhard, 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
DepositionApr 5, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 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)66,4738
Polymers65,7001
Non-polymers7737
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.535, 127.535, 106.785
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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: 65699.711 Da / Num. of mol.: 1 / Fragment: CATALYTIC SUBUNIT A (UNP residues 1-240, 617-964) / Mutation: G79R, F236A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: atpA, PH1975 / 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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 3.3 Å3/Da / Density % sol: 62.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 50%(v/v) MPD, 0.1M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 6, 2008 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 37346 / Num. obs: 35285 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 10.2 % / Biso Wilson estimate: 41 Å2 / Rsym value: 0.064 / Net I/σ(I): 30.5
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 10.2 % / Num. unique all: 3658 / Rsym value: 0.436 / % possible all: 100

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Processing

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

1vdz


Resolution: 2.35→19.75 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.882 / SU B: 13.264 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.267 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27944 1853 5 %RANDOM
Rwork0.22204 ---
obs0.22867 35285 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.362 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.35→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4039 0 52 265 4356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224172
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.721.995655
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9455510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98323.672177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.57115734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2991533
X-RAY DIFFRACTIONr_chiral_restr0.1190.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213098
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_it0.8831.52564
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.65224159
X-RAY DIFFRACTIONr_scbond_it2.68831608
X-RAY DIFFRACTIONr_scangle_it4.4874.51496
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.348→2.408 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 127 -
Rwork0.239 2549 -
obs-2549 98.85 %
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)
10.6557-0.81470.30693.478-0.30190.1567-0.4683-0.3347-0.23210.83840.6155-0.0715-0.1634-0.1123-0.14720.44060.37140.11360.32220.0850.1347-25.0725-42.602430.5067
20.8497-0.96570.00891.2860.0050.0091-0.2379-0.21240.05170.21330.2575-0.04750.00560.0214-0.01960.11160.1111-0.01270.1537-0.01440.0536-34.2944-26.667622.6886
30.6483-0.90410.01661.40.13310.4681-0.3594-0.27890.07750.38880.4103-0.13880.02150.1257-0.05090.26610.1696-0.03360.1972-0.05440.0397-27.4424-26.5525.5043
40.3581-0.20580.1710.9873-0.33430.5057-0.07590.03210.04090.02280.08040.045-0.00130.01-0.00460.0399-0.01370.00340.06410.00880.0588-49.1145-9.76716.2684
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A61 - 180
2X-RAY DIFFRACTION2A181 - 282
3X-RAY DIFFRACTION3A283 - 384
4X-RAY DIFFRACTION4A385 - 588

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