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- PDB-5cdf: Structure at 2.3 A of the alpha/beta monomer of the F-ATPase from... -

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Basic information

Entry
Database: PDB / ID: 5cdf
TitleStructure at 2.3 A of the alpha/beta monomer of the F-ATPase from Paracoccus denitrificans
Components
  • ATP synthase subunit alpha
  • ATP synthase subunit beta
KeywordsHYDROLASE
Function / homology
Function and homology information


proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, alpha subunit, C-terminal ...ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal 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. / Elongation Factor Tu (Ef-tu); domain 3 / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Thrombin, subunit H / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / 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
PHOSPHATE ION / ATP synthase subunit alpha / ATP synthase subunit beta
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMorales-Rios, E. / Montgomery, M.G. / Leslie, A.G.W. / Garcia-Trejo, J.J. / Walker, J.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
United Kingdom
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structure of a catalytic dimer of the alpha- and beta-subunits of the F-ATPase from Paracoccus denitrificans at 2.3 angstrom resolution.
Authors: Morales-Rios, E. / Montgomery, M.G. / Leslie, A.G. / Garcia-Trejo, J.J. / Walker, J.E.
History
DepositionJul 3, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP synthase subunit alpha
E: ATP synthase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,31711
Polymers105,4862
Non-polymers8329
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-25 kcal/mol
Surface area37180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.550, 102.920, 89.180
Angle α, β, γ (deg.)90.000, 112.670, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ATP synthase subunit alpha / ATP synthase F1 sector subunit alpha / F-ATPase subunit alpha


Mass: 55099.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria)
References: UniProt: A1B8N8, H+-transporting two-sector ATPase
#2: Protein ATP synthase subunit beta / ATP synthase F1 sector subunit beta / F-ATPase subunit beta


Mass: 50385.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria)
References: UniProt: A1B8P0, H+-transporting two-sector ATPase
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.91 Å3/Da / Density % sol: 57.77 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 7.8 / Details: PEG 10,000, cadaverine, Tris pH 7.8, glycerol, ATP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.3→33.55 Å / Num. obs: 48901 / % possible obs: 91.4 % / Redundancy: 2.9 % / CC1/2: 0.984 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.094 / Net I/σ(I): 5.5 / Num. measured all: 142669 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.3-2.372.80.5251.91240843810.6030.36494.1
9.48-33.553.20.06113.522817190.9850.04190.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
Aimless0.3.11data scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JDI

2jdi


Resolution: 2.3→33.55 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.2439 / WRfactor Rwork: 0.2122 / FOM work R set: 0.7744 / SU B: 9.361 / SU ML: 0.212 / SU R Cruickshank DPI: 0.3504 / SU Rfree: 0.2449 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.35 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2567 2427 5 %RANDOM
Rwork0.2252 ---
obs0.2268 46474 90.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.13 Å2 / Biso mean: 35.503 Å2 / Biso min: 16.15 Å2
Baniso -1Baniso -2Baniso -3
1--2.4 Å20 Å20.28 Å2
2---1.31 Å2-0 Å2
3---2.58 Å2
Refinement stepCycle: final / Resolution: 2.3→33.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7112 0 53 79 7244
Biso mean--45.09 26.55 -
Num. residues----944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197268
X-RAY DIFFRACTIONr_bond_other_d0.0010.027151
X-RAY DIFFRACTIONr_angle_refined_deg1.0651.9829833
X-RAY DIFFRACTIONr_angle_other_deg0.851316434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2675942
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89724.638304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.256151243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8261549
X-RAY DIFFRACTIONr_chiral_restr0.0570.21153
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218244
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021527
X-RAY DIFFRACTIONr_mcbond_it0.8873.5513774
X-RAY DIFFRACTIONr_mcbond_other0.8883.5513773
X-RAY DIFFRACTIONr_mcangle_it1.635.3194711
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 178 -
Rwork0.32 3554 -
all-3732 -
obs--94.1 %

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