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Yorodumi- PDB-4yb8: Ca. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yb8 | ||||||
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Title | Ca. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme A synthetase 1 in complex with phosphate and ADP | ||||||
Components |
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Keywords | LIGASE / 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: 1.9 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 | 4yb8.cif.gz | 498.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yb8.ent.gz | 425.3 KB | Display | PDB format |
PDBx/mmJSON format | 4yb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/4yb8 ftp://data.pdbj.org/pub/pdb/validation_reports/yb/4yb8 | HTTPS FTP |
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-Related structure data
Related structure data | 4xylC 4xymC 4xz3C 4y8vC 4yajC 4yakC 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
-Protein , 2 types, 4 molecules ACBD
#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 / 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 |
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-Non-polymers , 5 types, 302 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.94 % / Description: rod-like appearance |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / Details: 100 mM Tris/HCl pH 8.7, 14% (w/v) PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.984 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→110.61 Å / Num. all: 116787 / Num. obs: 116787 / % possible obs: 100 % / Redundancy: 13 % / Rmerge(I) obs: 0.165 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 9.8 % / Rmerge(I) obs: 4.603 / Mean I/σ(I) obs: 0.5 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→83.043 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.85 / 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: 1.9→83.043 Å
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Refine LS restraints |
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LS refinement shell |
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