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- PDB-3e3z: Crystal structure of bovine coupling Factor B bound with phenylar... -

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Basic information

Entry
Database: PDB / ID: 3e3z
TitleCrystal structure of bovine coupling Factor B bound with phenylarsine oxide
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


ATP biosynthetic process / Formation of ATP by chemiosmotic coupling / Cristae formation / proton-transporting ATP synthase complex, coupling factor F(o) / 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
Phenylarsine oxide / ATP synthase subunit s, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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 8, 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 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 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)20,8294
Polymers20,5151
Non-polymers3143
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.122, 49.722, 36.902
Angle α, β, γ (deg.)90.000, 108.840, 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 (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 / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-PA0 / Phenylarsine oxide / oxo(phenyl)arsane / Phenylarsine oxide


Mass: 168.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5AsO
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8
Details: 50% PPG 400, 100 mM Tris-HCl pH 8.0, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.97946 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: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 19212 / % possible obs: 95.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.039 / Χ2: 1.004
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.7-1.763.30.11315681.02178.3
1.76-1.833.40.09817711.00789.3
1.83-1.913.60.0919210.99296.7
1.91-2.023.70.07719801.00899
2.02-2.143.70.06519700.98698.5
2.14-2.313.70.05819680.99698.6
2.31-2.543.70.05119851.00598.8
2.54-2.913.70.04719951.03199.3
2.91-3.663.60.03620260.99799.5
3.66-403.70.02720281.00298.3

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Phasing

PhasingMethod: molecular replacement

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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: 1.7→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.199 / WRfactor Rwork: 0.16 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.894 / SU B: 1.758 / SU ML: 0.06 / SU R Cruickshank DPI: 0.101 / SU Rfree: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.188 978 5.1 %RANDOM
Rwork0.149 ---
obs0.151 19208 95.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.46 Å2 / Biso mean: 8.605 Å2 / Biso min: 4.42 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å20 Å2-1.4 Å2
2---0.6 Å20 Å2
3----2.32 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1468 0 16 227 1711
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221516
X-RAY DIFFRACTIONr_bond_other_d0.0010.021072
X-RAY DIFFRACTIONr_angle_refined_deg1.411.9682042
X-RAY DIFFRACTIONr_angle_other_deg1.35432608
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2715182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24524.18974
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89815290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2891510
X-RAY DIFFRACTIONr_chiral_restr0.0880.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021660
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02312
X-RAY DIFFRACTIONr_mcbond_it0.851.5895
X-RAY DIFFRACTIONr_mcbond_other0.2381.5362
X-RAY DIFFRACTIONr_mcangle_it1.55121443
X-RAY DIFFRACTIONr_scbond_it2.6023621
X-RAY DIFFRACTIONr_scangle_it4.2864.5597
LS refinement shellResolution: 1.7→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 63 -
Rwork0.147 1061 -
all-1124 -
obs--75.89 %

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