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- PDB-7o0d: monomeric acetyl-CoA synthase in open conformation with methaneth... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7o0d | |||||||||
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Title | monomeric acetyl-CoA synthase in open conformation with methanethiol moiety of CoA bound to nickel proximal | |||||||||
![]() | CO-methylating acetyl-CoA synthase | |||||||||
![]() | OXIDOREDUCTASE / metalloprotein / nickel / acetogenesis / cluster A / ACS / CoA | |||||||||
Function / homology | ![]() CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / : / acetyl-CoA metabolic process / 4 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kreibich, J. / Jeoung, J.H. / Dobbek, H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Ligand binding at the Ni,Ni-[4Fe-4S] cluster of acetyl-CoA synthase Authors: Kreibich, J. / Jeoung, J.H. / Dobbek, H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 305.8 KB | Display | ![]() |
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PDB format | ![]() | 244.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 32.4 KB | Display | |
Data in CIF | ![]() | 46.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nypC ![]() 7nysC ![]() 7nz5C ![]() 1ru3S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 82484.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: acsB, CHY_1222 / Plasmid: pQE30 Details (production host): modified vector with twin-strep-tag and TEV cleavage site Production host: ![]() ![]() References: UniProt: Q3ACS4, CO-methylating acetyl-CoA synthase |
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-Non-polymers , 9 types, 314 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/MEE.gif)
![](data/chem/img/PG6.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/MEE.gif)
![](data/chem/img/PG6.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SF4 / | ||||||||||||||
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#3: Chemical | #4: Chemical | ChemComp-MEE / | #5: Chemical | ChemComp-PG6 / #6: Chemical | #7: Chemical | ChemComp-PEG / #8: Chemical | ChemComp-SO4 / #9: Chemical | #10: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.9 Å3/Da / Density % sol: 68.46 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop Details: 150 mM MES pH 6.0, 2 M ammonium sulfate, 5% v/v PEG 300, 5 mM CoA trilithium salt |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→48.88 Å / Num. obs: 56520 / % possible obs: 99.5 % / Redundancy: 2 % / Biso Wilson estimate: 44.44 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.027 / Rpim(I) all: 0.027 / Rrim(I) all: 0.038 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 2 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3807 / CC1/2: 0.613 / Rpim(I) all: 0.589 / Rrim(I) all: 0.833 / % possible all: 95.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1RU3 Resolution: 2.3→48.88 Å / SU ML: 0.2403 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3302 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.81 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→48.88 Å
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Refine LS restraints |
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LS refinement shell |
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