+Open data
-Basic information
Entry | Database: PDB / ID: 4xyl | ||||||
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Title | Ca. Korarchaeum cryptofilum ACD1 in complex with coenzyme A | ||||||
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: 1.95 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 | 4xyl.cif.gz | 500.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xyl.ent.gz | 417.6 KB | Display | PDB format |
PDBx/mmJSON format | 4xyl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xyl_validation.pdf.gz | 913.4 KB | Display | wwPDB validaton report |
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Full document | 4xyl_full_validation.pdf.gz | 924.4 KB | Display | |
Data in XML | 4xyl_validation.xml.gz | 49 KB | Display | |
Data in CIF | 4xyl_validation.cif.gz | 69.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/4xyl ftp://data.pdbj.org/pub/pdb/validation_reports/xy/4xyl | HTTPS FTP |
-Related structure data
Related structure data | 4xymC 4xz3C 4y8vC 4yajC 4yakC 4yb8C 4ybzC 5hbrC 1wr2S 2csuS C: citing same article (ref.) S: Starting model for refinement |
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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 | #4: Chemical | #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: 2.39 Å3/Da / Density % sol: 48.57 % / Description: rod-like appearance |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 100 mM Tris/HCl, pH 8.3; 16% (w/v) PEG 6000; 10 mM CaCl2 |
-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: 1.23953 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.23953 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→83.46 Å / Num. all: 105037 / Num. obs: 105037 / % possible obs: 99.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.246 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 6.6 % / Rmerge(I) obs: 3.178 / Mean I/σ(I) obs: 0.6 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CSU and 1WR2 Resolution: 1.95→83.456 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.66 / 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: 1.95→83.456 Å
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Refine LS restraints |
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LS refinement shell |
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