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- PDB-1kmh: Crystal Structure of spinach chloroplast F1-ATPase complexed with... -

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Basic information

Entry
Database: PDB / ID: 1kmh
TitleCrystal Structure of spinach chloroplast F1-ATPase complexed with tentoxin
Components
  • ATPase alpha subunit
  • ATPase beta subunit
KeywordsHYDROLASE / Protein-Inhibitor Complex
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
TENTOXIN / ATP synthase subunit beta, chloroplastic / ATP synthase subunit alpha, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsGroth, G.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Structure of spinach chloroplast F1-ATPase complexed with the phytopathogenic inhibitor tentoxin.
Authors: Groth, G.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: The Structure of the Chloroplast F1-ATPase at 3.2 A Resolution
Authors: Groth, G. / Pohl, E.
History
DepositionDec 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: diffrn_source / software / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _software.name ..._diffrn_source.pdbx_synchrotron_site / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE ASYMMETRIC UNIT ALSO CONTAINS 1/3 OF THE GAMMA AND 1/3 OF THE EPSILON UNIT OF CHLOROPLAST F1-ATPASE. BOTH GAMMA AND EPSILON WERE NOT RESOLVED IN THE STRUCTURE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATPase alpha subunit
B: ATPase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,8413
Polymers109,4272
Non-polymers4141
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-8 kcal/mol
Surface area38450 Å2
MethodPISA
2
A: ATPase alpha subunit
B: ATPase beta subunit
hetero molecules

A: ATPase alpha subunit
B: ATPase beta subunit
hetero molecules

A: ATPase alpha subunit
B: ATPase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)329,5249
Polymers328,2806
Non-polymers1,2433
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 area29390 Å2
ΔGint-80 kcal/mol
Surface area100280 Å2
MethodPISA
3
B: ATPase beta subunit
hetero molecules

A: ATPase alpha subunit


Theoretical massNumber of molelcules
Total (without water)109,8413
Polymers109,4272
Non-polymers4141
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
Buried area5050 Å2
ΔGint-17 kcal/mol
Surface area38170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.887, 146.887, 381.679
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein ATPase alpha subunit / ATP synthase alpha chain


Mass: 55505.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P06450, EC: 3.6.1.34
#2: Protein ATPase beta subunit / ATP synthase beta chain


Mass: 53921.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P00825, EC: 3.6.1.34
#3: Chemical ChemComp-TTX / TENTOXIN / Tentoxin


Mass: 414.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30N4O4 / Comment: toxin*YM

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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: 3.62 Å3/Da / Density % sol: 66.01 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: Lithium sulfate, HEPES, dithiotreitol, pH 7.5, MICRO BATCH, temperature 293K
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.05 mMprotein11
225 mMHEPES11pH7.5
31 mMdithiothreitol11
40.002 %(w/v)PMSF11
50.01 %(w/v)sodium azide11
61 mMADP11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8452 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 30, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8452 Å / Relative weight: 1
ReflectionResolution: 3.4→20 Å / Num. obs: 18266 / % possible obs: 92.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 88.3 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.43
Reflection shellResolution: 3.4→3.52 Å / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2.51 / Num. unique all: 1713 / % possible all: 79.9
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 19747
Reflection shell
*PLUS
% possible obs: 79.9 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
CNSrefinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FX0

1fx0


Resolution: 3.4→6 Å / Cor.coef. Fo:Fc: 0.841 / Cor.coef. Fo:Fc free: 0.825 / SU B: 97.548 / SU ML: 0.928 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.766 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31895 858 5.1 %RANDOM
Rwork0.29675 ---
obs0.29788 15805 92.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 134.533 Å2
Baniso -1Baniso -2Baniso -3
1--2.33 Å2-1.16 Å20 Å2
2---2.33 Å20 Å2
3---3.49 Å2
Refinement stepCycle: LAST / Resolution: 3.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7187 0 30 0 7217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0227326
X-RAY DIFFRACTIONr_bond_other_d0.0030.026895
X-RAY DIFFRACTIONr_angle_refined_deg1.9951.989930
X-RAY DIFFRACTIONr_angle_other_deg1.052316002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.5363942
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.954151368
X-RAY DIFFRACTIONr_chiral_restr0.1030.21164
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028189
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021400
X-RAY DIFFRACTIONr_nbd_refined0.2870.32546
X-RAY DIFFRACTIONr_nbd_other0.2890.39168
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.5442
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1540.523
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2980.384
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3930.3227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.56
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.8911.54679
X-RAY DIFFRACTIONr_mcangle_it5.37127540
X-RAY DIFFRACTIONr_scbond_it5.78132647
X-RAY DIFFRACTIONr_scangle_it9.9274.52390
X-RAY DIFFRACTIONr_rigid_bond_restr3.62127326
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded1.85927219
LS refinement shellResolution: 3.4→3.459 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.322 42
Rwork0.316 775
Refinement
*PLUS
Highest resolution: 3.4 Å / Lowest resolution: 6 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.025
X-RAY DIFFRACTIONr_angle_d1.995
LS refinement shell
*PLUS
Lowest resolution: 3.49 Å / Rfactor Rfree: 0.322 / Rfactor Rwork: 0.316 / Rfactor obs: 0.316

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