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- PDB-3lg8: Crystal structure of the C-terminal part of subunit E (E101-206) ... -

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Basic information

Entry
Database: PDB / ID: 3lg8
TitleCrystal structure of the C-terminal part of subunit E (E101-206) from Methanocaldococcus jannaschii of A1AO ATP synthase
ComponentsA-type ATP synthase subunit E
KeywordsHYDROLASE / Archaea / peripheral stalk / Structural protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


proton-transporting two-sector ATPase complex, catalytic domain / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP binding / plasma membrane
Similarity search - Function
F-type ATP synthase subunit B-like, membrane domain superfamily / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit
Similarity search - Domain/homology
A-type ATP synthase subunit E
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.1 Å
AuthorsBalakrishna, A.M. / Manimekalai, M.S.S. / Hunke, C. / Gayen, S. / Jeyakanthan, J. / Gruber, G.
Citation
Journal: J.Bioenerg.Biomembr. / Year: 2010
Title: Crystal and solution structure of the C-terminal part of the Methanocaldococcus jannaschii A1AO ATP synthase subunit E revealed by X-ray diffraction and small-angle X-ray scattering
Authors: Balakrishna, A.M. / Manimekalai, M.S.S. / Hunke, C. / Gayen, S. / Rossle, M. / Jeyakanthan, J. / Gruber, G.
#1: Journal: J.Mol.Biol. / Year: 2007
Title: Dimeric core structure of modular stator subunit E of archaeal H+ -ATPase
Authors: Lokanath, N.K. / Matsuura, Y. / Kuroishi, C. / Takahashi, N. / Kunishima, N.
History
DepositionJan 19, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Nov 1, 2023Group: Data collection / Database references / 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
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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: A-type ATP synthase subunit E
B: A-type ATP synthase subunit E


Theoretical massNumber of molelcules
Total (without water)23,7092
Polymers23,7092
Non-polymers00
Water00
1
A: A-type ATP synthase subunit E


Theoretical massNumber of molelcules
Total (without water)11,8551
Polymers11,8551
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: A-type ATP synthase subunit E


Theoretical massNumber of molelcules
Total (without water)11,8551
Polymers11,8551
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.658, 73.658, 149.643
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 105 - 200 / Label seq-ID: 5 - 100

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 11854.684 Da / Num. of mol.: 2 / Fragment: UNP residues 101-206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / Gene: atpE, MJ0220 / Plasmid: pET 9d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q57673

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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: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05M Cesium chloride, 0.1M MES monohydrate buffer (pH 6.5), 30% v/v Jeffamine M-600, 1mM TCEP, 0.1mM glycine, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 28, 2009 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.1→30 Å / Num. obs: 2125 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 27.35
Reflection shellResolution: 4.1→4.17 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.076 / Mean I/σ(I) obs: 26.35 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DM9

2dm9


Resolution: 4.1→24.27 Å / Cor.coef. Fo:Fc: 0.803 / Cor.coef. Fo:Fc free: 0.735 / Occupancy max: 1 / Occupancy min: 1 / SU B: 108.693 / SU ML: 1.483 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. Only the Back bone atoms for all the residues were assigned since the side chains are not visible in the electron density map. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U ...Details: 1. Only the Back bone atoms for all the residues were assigned since the side chains are not visible in the electron density map. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.381 201 9.5 %RANDOM
Rwork0.353 ---
obs0.356 2125 99.58 %-
all-4717 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.6 Å2 / Biso mean: 30.022 Å2 / Biso min: 14.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 4.1→24.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1044 0 0 0 1044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.021042
X-RAY DIFFRACTIONr_angle_refined_deg0.8471.9421446
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9185210
X-RAY DIFFRACTIONr_chiral_restr0.0460.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02840
Refine LS restraints NCSNumber: 472 / Type: MEDIUM POSITIONAL / Rms dev position: 0.33 Å / Weight position: 0.5
LS refinement shellResolution: 4.103→4.318 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.451 25 -
Rwork0.408 260 -
all-285 -
obs--99.65 %

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