+Open data
-Basic information
Entry | Database: PDB / ID: 5ff5 | ||||||
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Title | Crystal Structure of SeMet PaaA | ||||||
Components | PaaA | ||||||
Keywords | TRANSFERASE / Adenylyltransferase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterobacter agglomerans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.933 Å | ||||||
Authors | Biernat, K.B. / Redinbo, M.R. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2016 Title: Post-translational Claisen Condensation and Decarboxylation en Route to the Bicyclic Core of Pantocin A. Authors: Ghodge, S.V. / Biernat, K.A. / Bassett, S.J. / Redinbo, M.R. / Bowers, A.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ff5.cif.gz | 128.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ff5.ent.gz | 104 KB | Display | PDB format |
PDBx/mmJSON format | 5ff5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/5ff5 ftp://data.pdbj.org/pub/pdb/validation_reports/ff/5ff5 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43168.020 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter agglomerans (bacteria) / Gene: paaA / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: Q9ZAR3 #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-NI / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, magnesium sulfate, glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.979 Å | |||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 15, 2015 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.93→29.48 Å / Num. obs: 16878 / % possible obs: 99.7 % / Redundancy: 25.3 % / Biso Wilson estimate: 66.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.024 / Net I/σ(I): 24.9 / Num. measured all: 427046 / Scaling rejects: 1 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.933→29.475 Å / FOM work R set: 0.7379 / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.54 / Stereochemistry target values: MLHL
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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 max: 126.93 Å2 / Biso mean: 57.48 Å2 / Biso min: 20 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.933→29.475 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
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