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- PDB-5x09: Crystal structure of subunit A mutant P235A/S238C of the A-ATP sy... -

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Basic information

Entry
Database: PDB / ID: 5x09
TitleCrystal structure of subunit A mutant P235A/S238C of the A-ATP synthase from pyrococcus horikoshii OT3
ComponentsV-type ATP synthase alpha chain,V-type ATP synthase alpha chain
KeywordsHYDROLASE / P LOOP / Proline mutant / serine mutant
Function / homology
Function and homology information


intron homing / intein-mediated protein splicing / plasma membrane ATP synthesis coupled proton transport / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / Hydrolases; Acting on ester bonds / endonuclease activity / ATP binding
Similarity search - Function
ATPsynthase alpha/beta subunit N-term extension / ATPsynthase alpha/beta subunit, N-terminal extension / V-type ATP synthase catalytic alpha chain / 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 motif profile. / Intein C-terminal splicing region / Hint (Hedgehog/Intein) domain C-terminal region ...ATPsynthase alpha/beta subunit N-term extension / ATPsynthase alpha/beta subunit, N-terminal extension / V-type ATP synthase catalytic alpha chain / 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 motif profile. / Intein C-terminal splicing region / Hint (Hedgehog/Intein) domain C-terminal region / Hint domain C-terminal / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain N-terminal / Hint domain superfamily / Homing endonuclease / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATP synthase alpha/beta family, beta-barrel domain / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha and beta subunits signature. / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / V-type ATP synthase alpha chain
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsDhirendra, S. / Gruber, G.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of educationMOE2011-T2-2-156; ARC 18/12 Singapore
CitationJournal: J. Struct. Biol. / Year: 2018
Title: Crystallographic and enzymatic insights into the mechanisms of Mg-ADP inhibition in the A1 complex of the A1AO ATP synthase
Authors: Singh, D. / Gruber, G.
History
DepositionJan 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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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,V-type ATP synthase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8145
Polymers60,4531
Non-polymers3604
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-9 kcal/mol
Surface area25400 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)127.467, 127.467, 105.349
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,V-type ATP synthase alpha chain / V-ATPase subunit A


Mass: 60453.336 Da / Num. of mol.: 1 / Fragment: UNP residues 51-240,UNP residues 617-964 / Mutation: G79R, P235A, S238C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
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-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 3.54 Å3/Da / Density % sol: 65.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 50%(v/v) MPD, 0.1M acetate buffer pH 4.5

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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: Mar 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→90.13 Å / Num. obs: 36816 / % possible obs: 99.7 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.07
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.83 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
SCALAdata scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M4Y
Resolution: 2.35→30 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.908 / SU B: 6.608 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.281 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27239 1830 5 %RANDOM
Rwork0.23513 ---
obs0.23707 34785 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.719 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0 Å20 Å2
2---0.28 Å20 Å2
3---0.56 Å2
Refinement stepCycle: 1 / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4187 0 24 131 4342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194297
X-RAY DIFFRACTIONr_bond_other_d0.0010.024204
X-RAY DIFFRACTIONr_angle_refined_deg1.0691.9825819
X-RAY DIFFRACTIONr_angle_other_deg0.71739692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7145528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42523.529187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58615760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3671536
X-RAY DIFFRACTIONr_chiral_restr0.060.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214758
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02916
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_it2.9887.4692121
X-RAY DIFFRACTIONr_mcbond_other2.9897.4642117
X-RAY DIFFRACTIONr_mcangle_it4.95811.1832644
X-RAY DIFFRACTIONr_mcangle_other4.95711.1862645
X-RAY DIFFRACTIONr_scbond_it2.7487.592176
X-RAY DIFFRACTIONr_scbond_other2.7487.5912177
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.63211.2963176
X-RAY DIFFRACTIONr_long_range_B_refined8.44158.394952
X-RAY DIFFRACTIONr_long_range_B_other8.4458.3964953
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.349→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 125 -
Rwork0.257 2521 -
obs--99.59 %

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