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Open data
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Basic information
Entry | Database: PDB / ID: 7u6i | ||||||
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Title | HalB with glycine and succinate | ||||||
![]() | Halogenase B | ||||||
![]() | BIOSYNTHETIC PROTEIN | ||||||
Function / homology | GLYCINE / SUCCINIC ACID / ArpA protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Neugebauer, M.E. / Kissman, E.N. / Chang, M.C.Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Biocatalytic control of site-selectivity and chain length-selectivity in radical amino acid halogenases. Authors: Kissman, E.N. / Neugebauer, M.E. / Sumida, K.H. / Swenson, C.V. / Sambold, N.A. / Marchand, J.A. / Millar, D.C. / Chang, M.C.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 120.7 KB | Display | ![]() |
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PDB format | ![]() | 92.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 24 KB | Display | |
Data in CIF | ![]() | 35.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7u6hC ![]() 7u6jC ![]() 6nieS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28632.223 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-GLY / | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.16 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: Equal volumes of protein solution (SwHalB (2.5 mg/ml), lysine (3 mM), alpha-ketoglutarate (3 mM, pH 7)) and reservoir solution (succinate phosphate glycine (SPG) buffer (100 mM, pH 5.2), 18% ...Details: Equal volumes of protein solution (SwHalB (2.5 mg/ml), lysine (3 mM), alpha-ketoglutarate (3 mM, pH 7)) and reservoir solution (succinate phosphate glycine (SPG) buffer (100 mM, pH 5.2), 18% (w/v) PEG 1500) were mixed |
-Data collection
Diffraction | Mean temperature: 194 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→143.41 Å / Num. obs: 53826 / % possible obs: 99.8 % / Redundancy: 39.65 % / CC1/2: 1 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3989 / CC1/2: 0.706 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6NIE Resolution: 2.05→82.74 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.12 / 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: 112.59 Å2 / Biso mean: 47.3102 Å2 / Biso min: 22.59 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.05→82.74 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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