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- PDB-4tt3: The Pathway of Binding of the Intrinsically Disordered Mitochondr... -
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Basic information
Entry | Database: PDB / ID: 4tt3 | ||||||
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Title | The Pathway of Binding of the Intrinsically Disordered Mitochondrial Inhibitor Protein to F1-ATPase | ||||||
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![]() | HYDROLASE / inhibitor protein | ||||||
Function / homology | ![]() angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / negative regulation of hydrolase activity / heme biosynthetic process / : / : / Mitochondrial protein degradation / : ...angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / negative regulation of hydrolase activity / heme biosynthetic process / : / : / Mitochondrial protein degradation / : / negative regulation of endothelial cell proliferation / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / erythrocyte differentiation / ADP binding / ATPase binding / protein homotetramerization / calmodulin binding / structural molecule activity / cell surface / protein homodimerization activity / ATP hydrolysis activity / protein-containing complex / mitochondrion / ATP binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Bason, J.V. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E. | ||||||
![]() | ![]() Title: Pathway of binding of the intrinsically disordered mitochondrial inhibitor protein to F1-ATPase. Authors: Bason, J.V. / Montgomery, M.G. / Leslie, A.G. / Walker, J.E. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 597.3 KB | Display | ![]() |
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PDB format | ![]() | 483.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 97.9 KB | Display | |
Data in CIF | ![]() | 133.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4tsfC ![]() 2v7qS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-ATP synthase subunit ... , 3 types, 7 molecules ABCDEFG
#1: Protein | Mass: 55301.207 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 51615.684 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P00829, H+-transporting two-sector ATPase #3: Protein | | Mass: 30300.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Protein , 1 types, 3 molecules HIJ
#4: Protein | Mass: 7403.996 Da / Num. of mol.: 3 / Fragment: UNP residues 36-85 / Mutation: K39A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 40 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | ChemComp-MG / #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Sequence details | RESIDUE NUMBERING: BY CONVENTION, THE FIFTH AMINO ACID (SERINE) IN THE BETA SUBUNITS (CHAINS D,E,F) ...RESIDUE NUMBERING: BY CONVENTION |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.11 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 8.2 Details: PEG 4000, Tris-HCl, magnesium chloride, EDTA, ATP, NaCl, spermidine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 7, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 3.21→67.12 Å / Num. obs: 73010 / % possible obs: 97.5 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 3.21→3.28 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.3 / % possible all: 99.1 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 2v7q Resolution: 3.21→136.02 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.872 / SU B: 29.017 / SU ML: 0.479 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.552 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 179.61 Å2 / Biso mean: 93.079 Å2 / Biso min: 34.36 Å2
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Refinement step | Cycle: final / Resolution: 3.21→136.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.21→3.293 Å / Total num. of bins used: 20
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