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- PDB-3qia: Crystal structure of P-loop G237A mutant of subunit A of the A1AO... -

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Basic information

Entry
Database: PDB / ID: 3qia
TitleCrystal structure of P-loop G237A mutant of subunit A of the A1AO ATP synthase
ComponentsV-type ATP synthase alpha chain
KeywordsHYDROLASE / ATP Binding
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 / molecular replacement / Resolution: 2.6 Å
AuthorsRagunathan, P. / Manimekalai, M.S.S. / Jeyakanthan, J. / Gruber, G.
Citation
Journal: J.Mol.Biol. / Year: 2011
Title: Conserved glycine residues in the P-loop of ATP synthases form a doorframe for nucleotide entrance.
Authors: Priya, R. / Kumar, A. / Manimekalai, M.S. / 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, M.S.S. / Balakrishna, A.M. / Jeyakanthan, J. / Gruber, G.
#2: 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.S. / Balakrishna, A.M. / Priya, R. / Biukovic, G. / Jeyakanthan, J. / Gruber, G.
#3: Journal: Acta Crystallogr.,Sect.C / 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
DepositionJan 26, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
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)66,70513
Polymers65,6901
Non-polymers1,01512
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.688, 128.688, 106.292
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: 65689.688 Da / Num. of mol.: 1 / Fragment: CATALYTIC SUBUNIT A (UNP residues 1-240, 617-964) / Mutation: G237A
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.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H4O2
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 3.35 Å3/Da / Density % sol: 63.28 % / Mosaicity: 0.293 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 50% (v/v) MPD, 2mM MgADP and 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: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2009 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 28040 / Num. obs: 27986 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 57.45 Å2 / Rmerge(I) obs: 0.061 / Χ2: 1.014 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.697.10.4527381.0641100
2.69-2.87.20.33727460.9811100
2.8-2.937.20.25127540.9581100
2.93-3.087.30.1827550.9631100
3.08-3.287.30.11627631.0051100
3.28-3.537.30.07327670.9661100
3.53-3.887.20.04828051.0081100
3.88-4.4470.04928181.0371100
4.44-5.596.60.04528481.0741100
5.59-306.60.01729921.095199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VDZ

1vdz


Resolution: 2.6→27.32 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.881 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 23.547 / SU ML: 0.232 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.496 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.29668 1406 5 %RANDOM
Rwork0.24015 ---
obs0.24296 26519 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 238.6 Å2 / Biso mean: 66.382 Å2 / Biso min: 10.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.6→27.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4439 0 68 175 4682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224609
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1981.9916238
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5245568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89923.687198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.66315818
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5341537
X-RAY DIFFRACTIONr_chiral_restr0.0840.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213451
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_it0.5941.52841
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.124587
X-RAY DIFFRACTIONr_scbond_it1.07831768
X-RAY DIFFRACTIONr_scangle_it1.9384.51648
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 88 -
Rwork0.301 1886 -
obs--97.39 %
Refinement TLS params.Method: refined / Origin x: 23.2138 Å / Origin y: -35.4784 Å / Origin z: -6.0841 Å
111213212223313233
T0.2273 Å2-0.136 Å2-0.0113 Å2-0.2117 Å20.0152 Å2--0.103 Å2
L1.202 °20.9973 °20.2392 °2-1.091 °20.316 °2--0.2408 °2
S0.3534 Å °-0.2788 Å °-0.0041 Å °0.2037 Å °-0.3381 Å °0.0347 Å °-0.0563 Å °-0.0054 Å °-0.0154 Å °

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