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- PDB-1sky: CRYSTAL STRUCTURE OF THE NUCLEOTIDE FREE ALPHA3BETA3 SUB-COMPLEX ... -

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Basic information

Entry
Database: PDB / ID: 1sky
TitleCRYSTAL STRUCTURE OF THE NUCLEOTIDE FREE ALPHA3BETA3 SUB-COMPLEX OF F1-ATPASE FROM THE THERMOPHILIC BACILLUS PS3
Components(F1-ATPASE) x 2
KeywordsATP SYNTHASE / F1FO ATP SYNTHASE / F1-ATPASE / ALPHA3BETA3 SUBCOMPLEX OF F1-ATPASE / HYDROLASE
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 / ADP binding / 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
ATP synthase subunit beta / ATP synthase subunit alpha
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsShirakihara, Y. / Leslie, A.G.W. / Abrahams, J.P. / Walker, J.E. / Ueda, T. / Sekimoto, Y. / Kambara, M. / Saika, K. / Kagawa, Y. / Yoshida, M.
Citation
Journal: Structure / Year: 1997
Title: The crystal structure of the nucleotide-free alpha 3 beta 3 subcomplex of F1-ATPase from the thermophilic Bacillus PS3 is a symmetric trimer.
Authors: Shirakihara, Y. / Leslie, A.G. / Abrahams, J.P. / Walker, J.E. / Ueda, T. / Sekimoto, Y. / Kambara, M. / Saika, K. / Kagawa, Y. / Yoshida, M.
#1: Journal: Photon Factory Activity Report / Year: 1994
Title: X-Ray Crystal Analysis of Alpha3Beta3 Complex of F1-ATPase from a Thermophilic Bacterium Ps3
Authors: Shirakihara, Y. / Ueda, T. / Sekimoto, Y. / Yoshida, M. / Saika, K.
History
DepositionFeb 26, 1997Processing site: BNL
Revision 1.0Mar 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Mar 12, 2014Group: Other
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: F1-ATPASE
E: F1-ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8394
Polymers106,6462
Non-polymers1922
Water00
1
B: F1-ATPASE
E: F1-ATPASE
hetero molecules

B: F1-ATPASE
E: F1-ATPASE
hetero molecules

B: F1-ATPASE
E: F1-ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,51612
Polymers319,9396
Non-polymers5766
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area25010 Å2
ΔGint-176 kcal/mol
Surface area103520 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)159.500, 159.500, 159.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein F1-ATPASE / F1-ATP SYNTHASE


Mass: 54648.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: PS3 / Organ: HEART
Plasmid: PKK ALPHA FOR ALPHA SUBUNIT, PUC118BETA FOR BETA SUBUNIT
Production host: Escherichia coli (E. coli) / Strain (production host): DK8 / References: UniProt: P09219, EC: 3.6.1.34
#2: Protein F1-ATPASE / F1-ATP SYNTHASE


Mass: 51998.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: PS3 / Organ: HEART
Plasmid: PKK ALPHA FOR ALPHA SUBUNIT, PUC118BETA FOR BETA SUBUNIT
Production host: Escherichia coli (E. coli) / Strain (production host): DK8 / References: UniProt: P07677, EC: 3.6.1.34
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
Compound detailsALPHA3 BETA3 SUBCOMPLEX OF F1-ATPASE COMPRISES THREE ALPHA AND THREE BETA SUBUNITS. BECAUSE THE ...ALPHA3 BETA3 SUBCOMPLEX OF F1-ATPASE COMPRISES THREE ALPHA AND THREE BETA SUBUNITS. BECAUSE THE SUBCOMPLEX IS SYMMETRICAL, ONE ALPHA (CHAIN B) AND ONE BETA (CHAIN E) SUBUNITS ARE GIVEN. THE ENTIRE SUBCOMPLEX CAN BE FORMED USING THE TRANSFORMATIONS GIVEN IN REMARK 350.

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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: 3.2 Å3/Da / Density % sol: 61 %
Description: J.P. ABRAHAMS, A.G.W. LESLIE, R. LUTTER, J.E. WALKER STRUCTURE AT 2.8A RESOLUTION OF F1-ATPASE FROM BOVINE HEART MITOCHONDRIA, NATURE 370,621-628, (1994)
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8
Details: HANGING DROP WITH 9-11% PEG20000, 0.12 M SODIUM SULFATE AT PH8.0, EQUILIBRATED AGAINST PROTEIN FREE RESERVOIR WITH HIGHER PEG SOLUTION BY 2%. KEPT AT 15DEG., vapor diffusion - hanging drop, temperature 288K
Crystal grow
*PLUS
Temperature: 15 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19-11 %PEG200001drop
20.12 Msodium sulphate1drop
30.05 MTris-sulphate1drop
410 mg/mlprotein1drop
511-14 %PEG200001reservoir
60.12 Msodium sulphate1reservoir
70.05 MTris-sulphate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1
DetectorDetector: IMAGE PLATE / Date: May 24, 1994 / Details: MIRROR + MONOCHROMATOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 109106 / % possible obs: 99 % / Redundancy: 4.6 % / Biso Wilson estimate: 83 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 8.9
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.5 / % possible all: 98.1
Reflection
*PLUS
Num. obs: 22429 / Num. measured all: 109106
Reflection shell
*PLUS
% possible obs: 98.1 %

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Processing

Software
NameClassification
AMoREphasing
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
CCP4data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MITOCHODRIAL F1-ATPASE

Resolution: 3.2→6 Å
RfactorNum. reflection% reflectionSelection details
Rfree0.299 905 4.8 %DONE BY FREERFACMTZ
Rwork0.222 ---
obs0.222 18868 99.1 %-
Displacement parametersBiso mean: 68 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 3.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7289 0 10 0 7299
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.59
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.65
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.46
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 3.2→3.32 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.349 98 4.1 %
Rwork0.37 2232 -
obs--97.12 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.65
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.46
LS refinement shell
*PLUS
Rfactor Rwork: 0.37

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