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- PDB-4ybz: Ca. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ybz | ||||||
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Title | Ca. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme A synthetase 1 in complex with ADP and with phosphorylated phosphohistidine segment (site I orientation) | ||||||
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![]() | LIGASE / Dinucleotide forming acetyl-CoA synthetase / complex / ACD | ||||||
Function / homology | ![]() acetate-CoA ligase (ADP-forming) activity / nucleotide binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Korarchaeum cryptofilum | ||||||
Method | ![]() ![]() | ||||||
![]() | Weisse, R.H.-J. / Scheidig, A.J. | ||||||
![]() | ![]() Title: Structure of NDP-forming Acetyl-CoA synthetase ACD1 reveals a large rearrangement for phosphoryl transfer. Authors: Weie, R.H. / Faust, A. / Schmidt, M. / Schonheit, P. / Scheidig, A.J. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 503.2 KB | Display | ![]() |
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PDB format | ![]() | 429.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 777.2 KB | Display | ![]() |
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Full document | ![]() | 784.2 KB | Display | |
Data in XML | ![]() | 51.3 KB | Display | |
Data in CIF | ![]() | 72.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xylC ![]() 4xymC ![]() 4xz3C ![]() 4y8vC ![]() 4yajC ![]() 4yakC ![]() 4yb8C ![]() 5hbrC 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
#1: Protein | Mass: 49433.496 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: phosphorylated His254 Source: (gene. exp.) ![]() Strain: OPF8 / Gene: Kcr_0198 / Production host: ![]() ![]() #2: Protein | Mass: 25676.797 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: OPF8 / Gene: Kcr_0115 / Plasmid: pET17b / Production host: ![]() ![]() #3: Chemical | #4: Chemical | ChemComp-ADP / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.61 % / Description: rod-like appearance |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop Details: 100 mM Tris/HCl pH 8.5, 18% (w/v) PEG6000, 30 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→83.032 Å / Num. all: 85835 / Num. obs: 85835 / % possible obs: 99.5 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.202 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 6.9 % / Rmerge(I) obs: 2.233 / Mean I/σ(I) obs: 0.8 / % possible all: 99.1 |
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Processing
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Refinement | Resolution: 2.1→83.032 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.66 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→83.032 Å
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Refine LS restraints |
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LS refinement shell |
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