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- PDB-7sfn: Crystal structure of OlmO, a spirocyclase involved in the biosynt... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7sfn | |||||||||
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Title | Crystal structure of OlmO, a spirocyclase involved in the biosynthesis of oligomycin | |||||||||
![]() | OlmO - oligomycin spirocyclase | |||||||||
![]() | HYDROLASE / cyclase / spyrocyclase / oligomycin / calycin | |||||||||
Function / homology | D-MALATE / Uncharacterized protein![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bilyk, O. / Leadlay, P.F. / Dias, M.V.B. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Enzyme-Catalyzed Spiroacetal Formation in Polyketide Antibiotic Biosynthesis. Authors: Bilyk, O. / Oliveira, G.S. / de Angelo, R.M. / Almeida, M.O. / Honorio, K.M. / Leeper, F.J. / Dias, M.V.B. / Leadlay, P.F. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 145.6 KB | Display | ![]() |
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PDB format | ![]() | 113.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.3 KB | Display | ![]() |
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Full document | ![]() | 462.7 KB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 21.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7sfpC 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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Unit cell |
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Components
#1: Protein | Mass: 21560.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: Q93HI7 #2: Chemical | ChemComp-MLT / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 3 M Malic acid, pH = 6.0 pH = 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 R 100K-A / Detector: PIXEL / Date: Mar 25, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→49.1 Å / Num. obs: 23608 / % possible obs: 99.6 % / Redundancy: 9.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.025 / Rrim(I) all: 0.078 / Net I/σ(I): 17.6 / Num. measured all: 221286 / Scaling rejects: 40 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]()
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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: 130.2 Å2 / Biso mean: 50.5205 Å2 / Biso min: 29.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→43.73 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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Refinement TLS params. | Method: refined / Origin x: 14.9718 Å / Origin y: 3.3919 Å / Origin z: 133.0074 Å
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Refinement TLS group |
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