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- PDB-1l2p: ATP Synthase b Subunit Dimerization Domain -

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Basic information

Entry
Database: PDB / ID: 1l2p
TitleATP Synthase b Subunit Dimerization Domain
ComponentsATP Synthase B Chain
KeywordsHYDROLASE / alpha helix
Function / homology
Function and homology information


proton-transporting ATP synthase complex / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / plasma membrane
Similarity search - Function
F1F0 ATP synthase subunit B, membrane domain / ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ATP synthase subunit b
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.55 Å
AuthorsDel Rizzo, P.A. / Dunn, S.D. / Bi, Y. / Shilton, B.H.
CitationJournal: Biochemistry / Year: 2002
Title: The "second stalk" of Escherichia coli ATP synthase: structure of the isolated dimerization domain.
Authors: Del Rizzo, P.A. / Bi, Y. / Dunn, S.D. / Shilton, B.H.
History
DepositionFeb 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 14, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_remark
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). The biological unit is a dimer. However, the biological dimer is not contained in the crystal. The dimer model cannot be generated by a simple coordinate transformation of the crystal structure. The biological dimer can, however, be modelled based on the surface properties of the crystal structure, and on solution small-angle X-ray scattering data.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP Synthase B Chain


Theoretical massNumber of molelcules
Total (without water)7,0591
Polymers7,0591
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.700, 40.760, 42.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ATP Synthase B Chain


Mass: 7058.982 Da / Num. of mol.: 1 / Fragment: Dimerization Domain (residues 62-122)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pSD149 / Production host: Escherichia coli (E. coli) / Strain (production host): MM294 / References: UniProt: P0ABA0, EC: 3.6.3.34
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.18 Å3/Da / Density % sol: 43.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 30% ISOPROPANOL, 45% 2-METHYL-2,4-PENTANEDIOL, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 18.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mg/mlprotein1drop
245 %2-propanol1reservoir
330 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.99203 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 20, 2000
RadiationMonochromator: Horizontally Bent Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99203 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. all: 9429 / Num. obs: 9325 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.027 / Net I/σ(I): 25.1
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.117 / Num. unique all: 835 / % possible all: 91.8
Reflection
*PLUS
Num. obs: 9455 / % possible obs: 93.5 % / Rmerge(I) obs: 0.027
Reflection shell
*PLUS
% possible obs: 83.1 % / Rmerge(I) obs: 0.117

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.55→29.37 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 682817.73 / Data cutoff high rms absF: 682817.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.313 972 10.4 %RANDOM
Rwork0.282 ---
all0.285 9429 --
obs0.285 9325 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.0756 Å2 / ksol: 0.428013 e/Å3
Displacement parametersBiso mean: 29 Å2
Baniso -1Baniso -2Baniso -3
1-5.81 Å20 Å20 Å2
2--3.43 Å20 Å2
3----9.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.55→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms494 0 0 54 548
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d13.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.63
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it1.92
X-RAY DIFFRACTIONc_scbond_it3.362
X-RAY DIFFRACTIONc_scangle_it5.52.5
LS refinement shellResolution: 1.55→1.65 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.336 147 10.2 %
Rwork0.292 1295 -
obs-1442 93.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 29.4 Å / Rfactor all: 0.285 / Rfactor obs: 0.282 / Rfactor Rfree: 0.313 / Rfactor Rwork: 0.282
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg13.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.63
LS refinement shell
*PLUS
Rfactor Rfree: 0.336 / Rfactor Rwork: 0.292 / Rfactor obs: 0.292

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