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Yorodumi- PDB-4y8v: Ca. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4y8v | ||||||
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Title | Ca. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme A synthetase 1 in complex with ADP and additional ADP bound to phosphate binding site | ||||||
Components |
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Keywords | TRANSFERASE / Dinucleotide forming acetyl-CoA synthetase / complex / ACD | ||||||
Function / homology | Function and homology information acetate-CoA ligase (ADP-forming) activity / nucleotide binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Korarchaeum cryptofilum | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 Å | ||||||
Authors | Weisse, R.H.-J. / Scheidig, A.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y8v.cif.gz | 513.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y8v.ent.gz | 424.4 KB | Display | PDB format |
PDBx/mmJSON format | 4y8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4y8v_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 4y8v_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 4y8v_validation.xml.gz | 52.2 KB | Display | |
Data in CIF | 4y8v_validation.cif.gz | 73.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/4y8v ftp://data.pdbj.org/pub/pdb/validation_reports/y8/4y8v | HTTPS FTP |
-Related structure data
Related structure data | 4xylC 4xymC 4xz3C 4yajC 4yakC 4yb8C 4ybzC 5hbrC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 49354.523 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Korarchaeum cryptofilum (strain OPF8) (archaea) Gene: Kcr_0198 / Plasmid: pET17b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1L3C9 #2: Protein | Mass: 25676.797 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Korarchaeum cryptofilum (strain OPF8) (archaea) Gene: Kcr_0115 / Plasmid: pET17b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1L7P8 #3: Chemical | ChemComp-ADP / #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.7 % / Description: rod-like |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / Details: 100 mM Tris/HCl pH8.3, 16% (w/v) PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.98 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.099→49.211 Å / Num. all: 86108 / Num. obs: 86108 / % possible obs: 97.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.167 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.242 / Mean I/σ(I) obs: 1.1 / % possible all: 77.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.099→49.211 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.33 / 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: 2.099→49.211 Å
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Refine LS restraints |
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LS refinement shell |
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