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- PDB-5bo5: Structure of a unique ATP synthase subunit NeqB from Nanoarcheaum... -

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Basic information

Entry
Database: PDB / ID: 5bo5
TitleStructure of a unique ATP synthase subunit NeqB from Nanoarcheaum equitans
ComponentsNEQ263
KeywordsHYDROLASE / ATP Synthase / Nanoarcheaum equitans / Catalytic core
Function / homology
Function and homology information


NeqB N-terminal domain / Rossmann fold - #12240 / V-type ATP synthase regulatory subunit B/beta / C-terminal domain of V and A type ATP synthase / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
V-type ATP synthase beta chain
Similarity search - Component
Biological speciesNanoarchaeum equitans Kin4-M (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.808 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 27, 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: NEQ263
B: NEQ263
C: NEQ263
D: NEQ263
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,13210
Polymers186,6994
Non-polymers4336
Water00
1
A: NEQ263
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7953
Polymers46,6751
Non-polymers1202
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16610 Å2
MethodPISA
2
B: NEQ263
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7953
Polymers46,6751
Non-polymers1202
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16250 Å2
MethodPISA
3
C: NEQ263
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7712
Polymers46,6751
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-13 kcal/mol
Surface area16320 Å2
MethodPISA
4
D: NEQ263
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7712
Polymers46,6751
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.229, 155.233, 177.451
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 29:49 or resseq 57:81 or resseq...
211chain 'B' and (resseq 29:49 or resseq 57:81 or resseq...
311chain 'C' and (resseq 29:49 or resseq 57:81 or resseq...
411chain 'D' and (resseq 29:49 or resseq 57:81 or resseq...

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Components

#1: Protein
NEQ263 / NeQB


Mass: 46674.777 Da / Num. of mol.: 4
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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / 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: 2.85 Å3/Da / Density % sol: 56.82 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / Details: 100mM HEPES, 200mM mgCl2, 30% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97928 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 50654 / % possible obs: 98.3 % / Redundancy: 13 % / Net I/σ(I): 23
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2 / % possible all: 91.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GQB

3gqb


Resolution: 2.808→29.78 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2568 1944 3.84 %
Rwork0.2161 --
obs0.2176 50654 95.85 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.101 Å2 / ksol: 0.336 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.4271 Å20 Å20 Å2
2--1.0855 Å20 Å2
3---7.3416 Å2
Refinement stepCycle: LAST / Resolution: 2.808→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12001 0 22 0 12023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912244
X-RAY DIFFRACTIONf_angle_d1.26216573
X-RAY DIFFRACTIONf_dihedral_angle_d12.8414564
X-RAY DIFFRACTIONf_chiral_restr0.0791894
X-RAY DIFFRACTIONf_plane_restr0.0082106
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2644X-RAY DIFFRACTIONPOSITIONAL0.07
12B2644X-RAY DIFFRACTIONPOSITIONAL0.07
13C2711X-RAY DIFFRACTIONPOSITIONAL0.109
14D2545X-RAY DIFFRACTIONPOSITIONAL0.071
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8083-2.87850.35741070.27452764X-RAY DIFFRACTION77
2.8785-2.95620.35691230.26673185X-RAY DIFFRACTION89
2.9562-3.04310.2931320.24613260X-RAY DIFFRACTION91
3.0431-3.14120.27211330.2443383X-RAY DIFFRACTION94
3.1412-3.25340.33951410.24493464X-RAY DIFFRACTION97
3.2534-3.38350.27131400.23913516X-RAY DIFFRACTION98
3.3835-3.53720.28841410.22913554X-RAY DIFFRACTION99
3.5372-3.72340.27871420.21483552X-RAY DIFFRACTION99
3.7234-3.95620.23531440.20933589X-RAY DIFFRACTION99
3.9562-4.26080.23561460.2023615X-RAY DIFFRACTION100
4.2608-4.68810.2211460.17863641X-RAY DIFFRACTION100
4.6881-5.36310.20491470.19473648X-RAY DIFFRACTION100
5.3631-6.74390.32131470.23693697X-RAY DIFFRACTION100
6.7439-29.78160.21871550.20643842X-RAY DIFFRACTION100

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