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- PDB-3a5d: Inter-subunit interaction and quaternary rearrangement defined by... -
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Basic information
Entry | Database: PDB / ID: 3a5d | ||||||
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Title | Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase | ||||||
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![]() | HYDROLASE / V-ATPase / asymmetric / rotation / vacuolar type / ATP synthesis / ATP-binding / Hydrogen ion transport / Ion transport / Nucleotide-binding / Transport | ||||||
Function / homology | ![]() plant-type vacuole / vacuolar proton-transporting V-type ATPase complex / proton-transporting ATP synthase complex / vacuolar acidification / fungal-type vacuole membrane / proton motive force-driven plasma membrane ATP synthesis / H+-transporting two-sector ATPase / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism ...plant-type vacuole / vacuolar proton-transporting V-type ATPase complex / proton-transporting ATP synthase complex / vacuolar acidification / fungal-type vacuole membrane / proton motive force-driven plasma membrane ATP synthesis / H+-transporting two-sector ATPase / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / lysosomal membrane / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Numoto, N. / Hasegawa, Y. / Takeda, K. / Miki, K. | ||||||
![]() | ![]() Title: Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase Authors: Numoto, N. / Hasegawa, Y. / Takeda, K. / Miki, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 856.2 KB | Display | ![]() |
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PDB format | ![]() | 578.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 557 KB | Display | ![]() |
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Full document | ![]() | 755 KB | Display | |
Data in XML | ![]() | 187.1 KB | Display | |
Data in CIF | ![]() | 264.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3a5cC ![]() 2hldS C: citing same article ( 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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Components
#1: Protein | Mass: 63699.980 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q56403, H+-transporting two-sector ATPase #2: Protein | Mass: 53219.500 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q56404, H+-transporting two-sector ATPase #3: Protein | Mass: 24715.566 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O87880, H+-transporting two-sector ATPase #4: Protein | Mass: 11294.904 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P74903, H+-transporting two-sector ATPase |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 69.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 1.6M ammonium sulfate, 0.1M MES-NaOH (pH6.0), 10% dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: Oct 12, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 4.8→50 Å / Num. obs: 57305 / % possible obs: 95.2 % / Redundancy: 5.2 % / Rsym value: 0.068 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 4.8→4.97 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 5364 / Rsym value: 0.375 / % possible all: 89.8 |
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Processing
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Refinement | Method to determine structure: Combination of molecular replacement, ![]() Starting model: PDB ENTRY 2HLD Resolution: 4.8→29.97 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 11714311.23 / Data cutoff low absF: 0 / Isotropic thermal model: DOMAIN / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL USED, REFINEMENTS WERE PERFORMED BY THE RIGID BODY AND B-DOMAIN REFINEMENTS. THE DOMAIN DEFINITIONS WERE SET TO FOUR DOMAINS IN THE A SUBUNIT (AI: RESIDUES 1-70; AII: 71- ...Details: BULK SOLVENT MODEL USED, REFINEMENTS WERE PERFORMED BY THE RIGID BODY AND B-DOMAIN REFINEMENTS. THE DOMAIN DEFINITIONS WERE SET TO FOUR DOMAINS IN THE A SUBUNIT (AI: RESIDUES 1-70; AII: 71-198; AIII; 199-429; AIV: 430-577), THREE IN THE B SUBUNIT (BI: 7-80; BII: 81-359; BIII; 360-463), TWO IN THE D SUBUNIT (DI: 1-55 AND DII: 132-205), AND TWO REGIONS OF F (FI: 1-75 AND FII: 76-104), RESPECTIVELY.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 207.809 Å2 / ksol: 0.1 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 191.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 4.8→29.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.8→4.97 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 10
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Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: protein.top |