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Yorodumi- PDB-7a9i: Crystal structure of Coronafacic Acid Ligase from Pectobacterium ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7a9i | ||||||
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Title | Crystal structure of Coronafacic Acid Ligase from Pectobacterium brasiliense | ||||||
Components | Cfl | ||||||
Keywords | LIGASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pectobacterium brasiliense (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Levy, C.W. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nature / Year: 2021 Title: Discovery, characterization and engineering of ligases for amide synthesis. Authors: Winn, M. / Rowlinson, M. / Wang, F. / Bering, L. / Francis, D. / Levy, C. / Micklefield, J. #1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7a9i.cif.gz | 259.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a9i.ent.gz | 173.2 KB | Display | PDB format |
PDBx/mmJSON format | 7a9i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7a9i_validation.pdf.gz | 456.7 KB | Display | wwPDB validaton report |
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Full document | 7a9i_full_validation.pdf.gz | 461 KB | Display | |
Data in XML | 7a9i_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 7a9i_validation.cif.gz | 31.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/7a9i ftp://data.pdbj.org/pub/pdb/validation_reports/a9/7a9i | HTTPS FTP |
-Related 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: 60406.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pectobacterium brasiliense (bacteria) / Gene: cfl, KCO_08370, KU74_07105 / Production host: Escherichia coli (E. coli) / References: UniProt: M4GWN4 | ||||
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#2: Chemical | ChemComp-R4Z / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.31 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 2M ammonium sulfate, 0.1M sodium Hepes pH 7.5, 2% v/v Peg 400 Temp details: Cold room |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→64.51 Å / Num. obs: 37973 / % possible obs: 99.82 % / Redundancy: 6.4 % / Biso Wilson estimate: 42.68 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.043 / Net I/σ(I): 8.07 |
Reflection shell | Resolution: 2.1→2.175 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.252 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3717 / CC1/2: 0.742 / CC star: 0.923 / Rpim(I) all: 0.5237 / % possible all: 99.38 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: inhouse Resolution: 2.1→64.51 Å / SU ML: 0.239 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.0074 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: 55.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→64.51 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A
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