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- PDB-3e4g: Crystal structure of bovine coupling Factor B, G28E mutant -

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Basic information

Entry
Database: PDB / ID: 3e4g
TitleCrystal structure of bovine coupling Factor B, G28E mutant
ComponentsATP synthase subunit s, mitochondrial
KeywordsELECTRON TRANSPORT / leucine-rich repeat / CF0 / Hydrogen ion transport / Inner membrane / Ion transport / Membrane / Mitochondrion / Transit peptide / Transport
Function / homology
Function and homology information


Formation of ATP by chemiosmotic coupling / Cristae formation / ATP biosynthetic process / proton-transporting ATP synthase complex / proton transmembrane transport / mitochondrial inner membrane / metal ion binding / cytoplasm
Similarity search - Function
Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
ATP synthase subunit s, mitochondrial
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.96 Å
AuthorsStroud, R.M. / Lee, J.K. / Belogrudov, G.I.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Crystal structure of bovine mitochondrial factor B at 0.96-A resolution.
Authors: Lee, J.K. / Belogrudov, G.I. / Stroud, R.M.
History
DepositionAug 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP synthase subunit s, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6613
Polymers20,5151
Non-polymers1462
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.476, 50.010, 36.886
Angle α, β, γ (deg.)90.000, 109.370, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ATP synthase subunit s, mitochondrial / ATP synthase-coupling factor B / Mitochondrial ATP synthase regulatory component factor B


Mass: 20514.738 Da / Num. of mol.: 1 / Mutation: G28E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: ATP5S, ATPW / Plasmid: pET43 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P22027, H+-transporting two-sector ATPase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.28 Å3/Da / Density % sol: 46.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.4
Details: 50% PPG 400, 100 mM Tris-HCl pH 7.4, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 12, 2007 / Details: KOHZU
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 0.955→50.7 Å / Num. all: 95943 / Num. obs: 92547 / % possible obs: 99.99 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 9.763 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 15.7
Reflection shellResolution: 0.955→0.985 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2 / Num. unique all: 1198 / Rsym value: 0.33 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å34.8 Å
Translation2.5 Å34.8 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DZE

3dze


Resolution: 0.96→30 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.174 / WRfactor Rwork: 0.151 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.924 / SU B: 0.49 / SU ML: 0.012 / SU R Cruickshank DPI: 0.022 / SU Rfree: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.022 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.164 4823 5 %RANDOM
Rwork0.143 ---
obs0.144 91066 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.3 Å2 / Biso mean: 14.542 Å2 / Biso min: 5.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20.05 Å2
2--0.14 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 0.96→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1508 0 9 265 1782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0221557
X-RAY DIFFRACTIONr_bond_other_d0.0040.021097
X-RAY DIFFRACTIONr_angle_refined_deg2.121.9662109
X-RAY DIFFRACTIONr_angle_other_deg2.14432687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2385195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70424.34276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.26515306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.6391510
X-RAY DIFFRACTIONr_chiral_restr0.150.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021711
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02311
X-RAY DIFFRACTIONr_mcbond_it2.2171.5920
X-RAY DIFFRACTIONr_mcbond_other1.1071.5369
X-RAY DIFFRACTIONr_mcangle_it3.27421493
X-RAY DIFFRACTIONr_scbond_it4.6993637
X-RAY DIFFRACTIONr_scangle_it6.5454.5608
X-RAY DIFFRACTIONr_rigid_bond_restr2.26832654
X-RAY DIFFRACTIONr_sphericity_free14.163266
X-RAY DIFFRACTIONr_sphericity_bonded6.35432614
LS refinement shellResolution: 0.96→0.985 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.797 65 -
Rwork0.782 1198 -
all-1263 -
obs--100 %

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