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- PDB-3lg8: Crystal structure of the C-terminal part of subunit E (E101-206) ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3lg8 | ||||||
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Title | Crystal structure of the C-terminal part of subunit E (E101-206) from Methanocaldococcus jannaschii of A1AO ATP synthase | ||||||
![]() | A-type ATP synthase subunit E | ||||||
![]() | HYDROLASE / Archaea / peripheral stalk / Structural protein / TRANSPORT PROTEIN | ||||||
Function / homology | ![]() 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 Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Balakrishna, A.M. / Manimekalai, M.S.S. / Hunke, C. / Gayen, S. / Jeyakanthan, J. / Gruber, G. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 44 KB | Display | ![]() |
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PDB format | ![]() | 27.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 408.9 KB | Display | ![]() |
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Full document | ![]() | 408.9 KB | Display | |
Data in XML | ![]() | 8 KB | Display | |
Data in CIF | ![]() | 10 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2dm9S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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
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Components
#1: Protein | Mass: 11854.684 Da / Num. of mol.: 2 / Fragment: UNP residues 101-206 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43067 / Gene: atpE, MJ0220 / Plasmid: pET 9d / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.23 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 28, 2009 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 4.1→4.17 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.076 / Mean I/σ(I) obs: 26.35 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.6 Å2 / Biso mean: 30.022 Å2 / Biso min: 14.24 Å2
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Refinement step | Cycle: LAST / Resolution: 4.1→24.27 Å
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Refine LS restraints |
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Refine LS restraints NCS | Number: 472 / Type: MEDIUM POSITIONAL / Rms dev position: 0.33 Å / Weight position: 0.5 | ||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 4.103→4.318 Å / Total num. of bins used: 10
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