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- PDB-1fx0: Crystal structure of the chloroplast F1-ATPase from spinach -

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Basic information

Entry
Database: PDB / ID: 1fx0
TitleCrystal structure of the chloroplast F1-ATPase from spinach
Components
  • ATP SYNTHASE ALPHA CHAIN
  • ATP SYNTHASE BETA CHAIN
KeywordsHYDROLASE / latent ATPase / thermal stability / potential tentoxin binding site
Function / homology
Function and homology information


mitochondrial proton-transporting ATP synthase complex / chloroplast thylakoid membrane / proton motive force-driven mitochondrial ATP synthesis / proton motive force-driven ATP synthesis / 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 / ADP binding / ATP hydrolysis activity / ATP binding
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, F1 complex, alpha subunit ...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 / 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 / Elongation Factor Tu (Ef-tu); domain 3 / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ATP synthase subunit beta, chloroplastic / ATP synthase subunit alpha, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsGroth, G. / Pohl, E.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: The structure of the chloroplast F1-ATPase at 3.2 A resolution.
Authors: Groth, G. / Pohl, E.
#1: Journal: Eur.J.Biochem. / Year: 1999
Title: Rapid Purification of Membrane extrinsic F1-domain of chloroplast ATP synthase in monodisperse form suitable for 3D crystallization
Authors: Groth, G. / Schirwitz, K.
History
DepositionSep 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation
Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP SYNTHASE ALPHA CHAIN
B: ATP SYNTHASE BETA CHAIN


Theoretical massNumber of molelcules
Total (without water)109,4272
Polymers109,4272
Non-polymers00
Water0
1
A: ATP SYNTHASE ALPHA CHAIN
B: ATP SYNTHASE BETA CHAIN

A: ATP SYNTHASE ALPHA CHAIN
B: ATP SYNTHASE BETA CHAIN

A: ATP SYNTHASE ALPHA CHAIN
B: ATP SYNTHASE BETA CHAIN


Theoretical massNumber of molelcules
Total (without water)328,2806
Polymers328,2806
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area27280 Å2
ΔGint-97 kcal/mol
Surface area101910 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)147.700, 147.700, 385.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsThe biological assembly is a Hetero-Hexamer containing 3 copies of the A and 3 copies of the B subunit The asymmetric unit contains also one third of the gamma and one third of the epsilon subunit. The structures of these subunits, however, were not resolved. The heterohexamer consist of 3x(alpha), 3x(beta), 1x(gamma), 1x(epsilon).

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Components

#1: Protein ATP SYNTHASE ALPHA CHAIN


Mass: 55505.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06450, EC: 3.6.1.34
#2: Protein ATP SYNTHASE BETA CHAIN


Mass: 53921.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P00825, EC: 3.6.1.34

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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: 3.69 Å3/Da / Density % sol: 66.7 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 7.5
Details: ammonium sulfate, HEPES, Na-azide, pH 7.5, Microbatch, temperature 25K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mMHEPES11
21 mMdithiothreitol11
30.002 %(w/v)PMSF11
40.01 %(w/v)11NaN3
51.5 Mammonium sulfate11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 14, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 3.2→20 Å / Num. all: 23315 / Num. obs: 23050 / % possible obs: 86.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.9 % / Biso Wilson estimate: 73.54 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 6.4
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 2 % / Rmerge(I) obs: 0.288 / % possible all: 76
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 231238

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
TRUNCATEdata reduction
AMoREphasing
CNSrefinement
CCP4(TRUNCATE)data scaling
RefinementResolution: 3.2→6 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.35 924 random
Rwork0.3191 --
all-22819 -
obs-22819 -
Refinement stepCycle: LAST / Resolution: 3.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7187 0 0 0 7187
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005408
X-RAY DIFFRACTIONc_angle_deg1.35434
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 6 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.319 / Rfactor Rfree: 0.35
Solvent computation
*PLUS
Displacement parameters
*PLUS

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