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- PDB-3e2j: Crystal structure of bovine coupling factor B -

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Basic information

Entry
Database: PDB / ID: 3e2j
TitleCrystal structure of bovine coupling factor B
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: 2.9 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 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _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
A: ATP synthase subunit s, mitochondrial
B: ATP synthase subunit s, mitochondrial
C: ATP synthase subunit s, mitochondrial
D: ATP synthase subunit s, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8688
Polymers81,7714
Non-polymers974
Water45025
1
A: ATP synthase subunit s, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4672
Polymers20,4431
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ATP synthase subunit s, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4672
Polymers20,4431
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ATP synthase subunit s, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4672
Polymers20,4431
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ATP synthase subunit s, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4672
Polymers20,4431
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.556, 133.941, 115.711
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 4 / Auth seq-ID: 1 - 175 / Label seq-ID: 2 - 176

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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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: 20442.676 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.4
Details: 45% PPG 400, 100 mM Bis-Tris pH 6.5, 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: 1.111 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 12, 2006 / Details: KOHZU
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.111 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 16810 / % possible obs: 95.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.076 / Χ2: 1.003
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.581 / Num. unique all: 1349 / Χ2: 1.006 / % possible all: 78.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 36.86 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.9 Å28.98 Å
Translation2.9 Å28.98 Å

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Processing

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

3dze


Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.854 / WRfactor Rfree: 0.314 / WRfactor Rwork: 0.223 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.724 / SU B: 24.598 / SU ML: 0.478 / SU Rfree: 0.585 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.585 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.329 840 5 %RANDOM
Rwork0.237 ---
obs0.241 16766 95.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.76 Å2 / Biso mean: 69.806 Å2 / Biso min: 29.83 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å20 Å2
2--4.9 Å20 Å2
3----3.8 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5598 0 4 25 5627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225723
X-RAY DIFFRACTIONr_angle_refined_deg1.7461.9527737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5985698
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.8524.391271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.468151020
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4971530
X-RAY DIFFRACTIONr_chiral_restr0.1070.2845
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214302
X-RAY DIFFRACTIONr_mcbond_it0.6921.53479
X-RAY DIFFRACTIONr_mcangle_it1.3325568
X-RAY DIFFRACTIONr_scbond_it1.75932244
X-RAY DIFFRACTIONr_scangle_it2.9624.52168
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1326 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
AMEDIUM POSITIONAL0.330.5
BMEDIUM POSITIONAL0.330.5
CMEDIUM POSITIONAL0.350.5
DMEDIUM POSITIONAL0.350.5
AMEDIUM THERMAL1.482
BMEDIUM THERMAL1.52
CMEDIUM THERMAL1.582
DMEDIUM THERMAL1.442
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 69 -
Rwork0.298 915 -
all-984 -
obs--77.3 %

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