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Yorodumi- PDB-7jlr: Crystal structure of Bacillus subtilis UppS in complex with JPD447 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jlr | |||||||||
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Title | Crystal structure of Bacillus subtilis UppS in complex with JPD447 | |||||||||
Components | Isoprenyl transferase | |||||||||
Keywords | TRANSFERASE / undecaprenyl / cis-prenyltransferase / carrier lipid / JPD447 | |||||||||
Function / homology | Function and homology information Z-farnesyl diphosphate synthase activity / polyprenyltransferase activity / di-trans,poly-cis-undecaprenyl-diphosphate synthase activity / polyprenol biosynthetic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / manganese ion binding / magnesium ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Workman, S.D. / Strynadka, N.C.J. | |||||||||
Funding support | Canada, 2items
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Citation | Journal: J.Med.Chem. / Year: 2021 Title: Structural Insights into the Inhibition of Undecaprenyl Pyrophosphate Synthase from Gram-Positive Bacteria. Authors: Workman, S.D. / Day, J. / Farha, M.A. / El Zahed, S.S. / Bon, C. / Brown, E.D. / Organ, M.G. / Strynadka, N.C.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jlr.cif.gz | 116 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jlr.ent.gz | 88.9 KB | Display | PDB format |
PDBx/mmJSON format | 7jlr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jlr_validation.pdf.gz | 667.1 KB | Display | wwPDB validaton report |
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Full document | 7jlr_full_validation.pdf.gz | 668.6 KB | Display | |
Data in XML | 7jlr_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 7jlr_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/7jlr ftp://data.pdbj.org/pub/pdb/validation_reports/jl/7jlr | HTTPS FTP |
-Related structure data
Related structure data | 7jliSC 7jljC 7jlmC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 29814.117 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) Gene: uppS, A3772_08985, B4122_2664, B4417_3501, BS16045_01759, ETA10_09020, ETK61_09295, GII79_08795, SC09_Contig19orf01203 Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A063XDJ9, Transferases; Transferring alkyl or aryl groups, other than methyl groups |
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#2: Chemical | ChemComp-V0D / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.6 % / Mosaicity: 0.19 ° |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 5.5 / Details: PEG 3000, NaCitrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 30, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→48.17 Å / Num. obs: 15845 / % possible obs: 100 % / Redundancy: 12.4 % / CC1/2: 1 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.024 / Rrim(I) all: 0.084 / Net I/σ(I): 17.3 / Num. measured all: 195859 / Scaling rejects: 1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7JLI Resolution: 2.2→42.51 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.47 / 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: 143.37 Å2 / Biso mean: 70.6329 Å2 / Biso min: 33.09 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→42.51 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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