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Yorodumi- PDB-8aqr: Native crystal structure of the N-terminal beta-hairpin docking (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8aqr | ||||||
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Title | Native crystal structure of the N-terminal beta-hairpin docking (bHD) domain of the AerJ halogenase, from the aeruginosin biosynthetic assembly line | ||||||
Components | AerJ | ||||||
Keywords | PROTEIN BINDING / beta-hairpin docking domain / nonribosomal peptide synthetase / polyketide synthase / halogenase | ||||||
Function / homology | TubC, N-terminal docking domain superfamily / TubC, N-terminal docking domain / TubC N-terminal docking domain / FAD-binding domain / FAD binding domain / FAD binding / FAD/NAD(P)-binding domain superfamily / AerJ Function and homology information | ||||||
Biological species | Microcystis aeruginosa NIES-98 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.46 Å | ||||||
Authors | Fage, C.D. / Lewandowski, J.R. / Challis, G.L. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Tandem halogenation and condensation in aeruginosin biosynthesis is directed by docking domain-mediated carrier protein recruitment Authors: Beech, M.J. / Fage, C.D. / Smith, H.G. / Kosol, S. / Gallo, A. / Bahia, D. / Jenner, M. / Lewandowski, J.R. / Challis, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8aqr.cif.gz | 95 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8aqr.ent.gz | 72.9 KB | Display | PDB format |
PDBx/mmJSON format | 8aqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/8aqr ftp://data.pdbj.org/pub/pdb/validation_reports/aq/8aqr | HTTPS FTP |
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-Related structure data
Related structure data | 8aqqC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 6732.778 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: Residues 1-56 of the AerJ halogenase, with an N-terminal Gly-Ser thrombin cleavage scar Source: (gene. exp.) Microcystis aeruginosa NIES-98 (bacteria) Gene: aerJ, BFG60_0936 / Plasmid: pET-24a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B9VVV3 #2: Chemical | ChemComp-CL / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.11 Å3/Da / Density % sol: 41.78 % / Description: Rectangular prism |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 0.1 M BICINE (pH 9.0), 2.4 M ammonium sulfate, final pH 9.0 |
-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: 0.91587 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 23, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.46→61.28 Å / Num. obs: 58560 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.045 / Rrim(I) all: 0.117 / Net I/σ(I): 10.9 / Num. measured all: 394159 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AerJ bHD domain, SeMet derivative Resolution: 1.46→61.28 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.06 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.01 Å2 / Biso mean: 29.5813 Å2 / Biso min: 15.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.46→61.28 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20
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