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- PDB-3p20: Crystal structure of vanadate bound subunit A of the A1AO ATP synthase -

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Basic information

Entry
Database: PDB / ID: 3p20
TitleCrystal structure of vanadate bound 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 / VANADATE ION / A-type ATP synthase subunit A
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å
AuthorsManimekalai, M.S.S. / Kumar, 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, M.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. / Balakrishna, A.M. / Priya, R. / Biukovic, G. / Jeyakanthan, J. / Gruber, G.
#3: 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
DepositionOct 1, 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 4, 2013Group: Database references
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Nov 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)66,84313
Polymers65,7761
Non-polymers1,06712
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.550, 127.550, 104.064
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 65775.805 Da / Num. of mol.: 1 / Fragment: CATALYTIC SUBUNIT (UNP residues 1-240, 617-964) / Mutation: 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 / 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

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Non-polymers , 5 types, 97 molecules

#2: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4
#3: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 3.22 Å3/Da / Density % sol: 61.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 50% (v/v) MPD, 2mM sodium orthovanadate, 2mM Magnesium chloride and 0.1M 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: BL12B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Feb 8, 2010 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→30 Å / Num. all: 20571 / Num. obs: 20534 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 69.93 Å2 / Rmerge(I) obs: 0.087 / Χ2: 0.593 / Net I/σ(I): 7.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.86-2.968.20.45820100.4491100
2.96-3.088.50.35620010.4541100
3.08-3.228.60.24920200.4731100
3.22-3.398.70.1720150.4681100
3.39-3.68.90.1220260.5111100
3.6-3.889.10.08920360.5211100
3.88-4.279.30.07220430.5851100
4.27-4.889.20.05820630.6421100
4.88-6.159.10.07621030.9361100
6.15-308.50.04322170.8331100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 32.79 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.85 Å29.65 Å
Translation2.85 Å29.65 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vdz

1vdz


Resolution: 2.85→29.25 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.897 / Occupancy max: 1 / Occupancy min: 1 / SU B: 22.74 / SU ML: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2457 1042 5.1 %RANDOM
Rwork0.2097 ---
obs0.2116 20488 99.99 %-
all-20534 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 168.33 Å2 / Biso mean: 50.3054 Å2 / Biso min: 4.09 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.85→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4086 0 66 85 4237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224235
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.9915733
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7115516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.78623.536181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.98315747
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7381535
X-RAY DIFFRACTIONr_chiral_restr0.1180.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213163
X-RAY DIFFRACTIONr_mcbond_it0.781.52606
X-RAY DIFFRACTIONr_mcangle_it1.51424214
X-RAY DIFFRACTIONr_scbond_it2.30831629
X-RAY DIFFRACTIONr_scangle_it4.1584.51519
LS refinement shellResolution: 2.855→2.928 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 80 -
Rwork0.265 1397 -
all-1477 -
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)
11.03661.571-1.25324.64730.36984.0407-0.39220.1266-0.2462-1.55790.4992-0.6214-0.43760.1048-0.1070.582-0.23380.17730.216-0.06680.1898-21.607932.0919-12.216
21.0731.0149-0.16731.7126-0.12160.0437-0.06620.12380.1085-0.07850.07820.113-0.00550.0208-0.0120.0546-0.0664-0.02170.13840.02970.0157-29.532338.00273.9368
310.1658-4.224-2.39912.4732-1.10636.74160.37581.5201-0.327-0.5856-0.48960.14051.1663-0.75440.11380.3103-0.0797-0.0310.33510.01780.1666-41.593223.5149-10.0472
40.78610.57280.54491.3702-0.09581.0876-0.16050.1872-0.1144-0.25080.2092-0.2688-0.02180.2484-0.04860.093-0.09130.0520.1819-0.05520.0762-24.484923.0271-1.4226
50.44030.2635-0.24090.7301-0.31360.3767-0.0554-0.0105-0.04770.03690.05280.02780.01990.06120.00270.03630.0083-0.00190.07290.00540.032-47.81710.346918.7082
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A62 - 114
2X-RAY DIFFRACTION2A115 - 258
3X-RAY DIFFRACTION3A259 - 284
4X-RAY DIFFRACTION4A285 - 377
5X-RAY DIFFRACTION5A378 - 588

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