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- PDB-5bn5: Structural basis for a unique ATP synthase core complex from Nano... -

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Basic information

Entry
Database: PDB / ID: 5bn5
TitleStructural basis for a unique ATP synthase core complex from Nanoarcheaum equitans
Components
  • NEQ263
  • V-type ATP synthase alpha chain
KeywordsHYDROLASE / ATP Synthase / Nanoarcheaum equitans / Catalytic core
Function / homology
Function and homology information


ATP biosynthetic process / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / ATP binding / plasma membrane
Similarity search - Function
NeqB N-terminal domain / Rossmann fold - #12240 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / V-type ATP synthase regulatory subunit B/beta / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit barrel-sandwich domain / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / : ...NeqB N-terminal domain / Rossmann fold - #12240 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / V-type ATP synthase regulatory subunit B/beta / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit barrel-sandwich domain / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid 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, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / 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
A-type ATP synthase subunit A / NEQ263
Similarity search - Component
Biological speciesNanoarchaeum equitans Kin4-M (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.997 Å
AuthorsMohanty, S. / Jobichen, C. / Chichili, V.P.R. / Sivaraman, J.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis for a Unique ATP Synthase Core Complex from Nanoarcheaum equitans
Authors: Mohanty, S. / Jobichen, C. / Chichili, V.P.R. / Velazquez-Campoy, A. / Low, B.C. / Hogue, C.W.V. / Sivaraman, J.
History
DepositionMay 25, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Nov 18, 2015Group: Database references
Revision 1.3Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: V-type ATP synthase alpha chain
B: NEQ263
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,5393
Polymers111,4432
Non-polymers961
Water00
1
A: V-type ATP synthase alpha chain
B: NEQ263
hetero molecules

A: V-type ATP synthase alpha chain
B: NEQ263
hetero molecules

A: V-type ATP synthase alpha chain
B: NEQ263
hetero molecules


Theoretical massNumber of molelcules
Total (without water)334,6179
Polymers334,3296
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_975-y+4,x-y+2,z1
crystal symmetry operation3_795-x+y+2,-x+4,z1
Unit cell
Length a, b, c (Å)192.649, 192.649, 108.566
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThe biological assembly is hetero-hexameric

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Components

#1: Protein V-type ATP synthase alpha chain / V-ATPase subunit A


Mass: 64768.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nanoarchaeum equitans Kin4-M (archaea) / Strain: Kin4-M / Gene: atpA, NEQ103
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG
References: UniProt: Q74MJ7, H+-transporting two-sector ATPase
#2: Protein NEQ263 / NeqB


Mass: 46674.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nanoarchaeum equitans Kin4-M (archaea) / Strain: Kin4-M / Gene: NEQ263
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q74MS5
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 64.75 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES, 1.6M Ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.157
ReflectionResolution: 3→33 Å / Num. obs: 29083 / % possible obs: 96.9 % / Redundancy: 4 % / Net I/σ(I): 5.3
Reflection shellResolution: 3→3.05 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.1 / % possible all: 87

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GQB

3gqb


Resolution: 2.997→32.108 Å / Cross valid method: FREE R-VALUE / σ(F): 2.09 / Phase error: 33.87 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2542 2039 7.01 %
Rwork0.2213 --
obs0.224 29083 96.45 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 7.97 Å2 / ksol: 0.322 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.7708 Å20 Å20 Å2
2---8.7708 Å20 Å2
3---17.5415 Å2
Refinement stepCycle: LAST / Resolution: 2.997→32.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7550 0 5 0 7555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027708
X-RAY DIFFRACTIONf_angle_d0.4810434
X-RAY DIFFRACTIONf_dihedral_angle_d8.8272896
X-RAY DIFFRACTIONf_chiral_restr0.0331176
X-RAY DIFFRACTIONf_plane_restr0.0031330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0019-3.07690.32881490.27691735X-RAY DIFFRACTION81
3.0769-3.15990.34351150.25631894X-RAY DIFFRACTION88
3.1599-3.25280.31191360.24691863X-RAY DIFFRACTION88
3.2528-3.35760.30521460.24051892X-RAY DIFFRACTION90
3.3576-3.47750.28491280.23051923X-RAY DIFFRACTION90
3.4775-3.61640.26831570.23381939X-RAY DIFFRACTION90
3.6164-3.78070.24381300.22131992X-RAY DIFFRACTION92
3.7807-3.97950.24691560.20631951X-RAY DIFFRACTION92
3.9795-4.22820.24411350.20481960X-RAY DIFFRACTION92
4.2282-4.55350.23251420.19711993X-RAY DIFFRACTION92
4.5535-5.00950.21931560.19761976X-RAY DIFFRACTION92
5.0095-5.72950.23721460.22291982X-RAY DIFFRACTION92
5.7295-7.20010.22771480.21611979X-RAY DIFFRACTION93
7.2001-28.88640.1981390.21661991X-RAY DIFFRACTION93

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