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Yorodumi- PDB-6szg: Acinetobacter baumannii undecaprenyl pyrophosphate synthase (AB-U... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6szg | ||||||
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Title | Acinetobacter baumannii undecaprenyl pyrophosphate synthase (AB-UppS) in complex with GR839 and GSK513 | ||||||
Components | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | ||||||
Keywords | TRANSFERASE / Inhibitor complex | ||||||
Function / homology | Function and homology information ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] / di-trans,poly-cis-undecaprenyl-diphosphate synthase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / magnesium ion binding Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Thorpe, J.H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2020 Title: Cocktailed fragment screening by X-ray crystallography of the antibacterial target undecaprenyl pyrophosphate synthase from Acinetobacter baumannii. Authors: Thorpe, J.H. / Wall, I.D. / Sinnamon, R.H. / Taylor, A.N. / Stavenger, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6szg.cif.gz | 114 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6szg.ent.gz | 84.7 KB | Display | PDB format |
PDBx/mmJSON format | 6szg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sz/6szg ftp://data.pdbj.org/pub/pdb/validation_reports/sz/6szg | HTTPS FTP |
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-Related structure data
Related structure data | 6szhC 1x07S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 30904.873 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) Gene: ispU, uppS, uppS_2, A7M79_11260, A7M90_02080, A7N09_13955, AB719_02530, B4R90_04635, B9X91_17010, B9X95_06890, BWP00_01470, CBE85_15965, CEJ63_18040, CSB70_2045, CYQ93_09555, D3X57_15480, DCD77_ ...Gene: ispU, uppS, uppS_2, A7M79_11260, A7M90_02080, A7N09_13955, AB719_02530, B4R90_04635, B9X91_17010, B9X95_06890, BWP00_01470, CBE85_15965, CEJ63_18040, CSB70_2045, CYQ93_09555, D3X57_15480, DCD77_00905, DOL94_09555, DVA79_11950, E2535_15455, E4664_05920, EA685_17420, EA722_15190, EHF38_07755, EJB02_03910, EWO92_00565, EWO96_03250, EWP49_03250, FDF20_10270, LV38_00732, NCTC13305_00281, SAMEA104305177_04421, SAMEA104305229_03969, SAMEA104305268_02140, SAMEA104305283_01949, SAMEA104305292_00210, SAMEA104305315_07345, SAMEA104305318_03206, SAMEA104305320_02219, SAMEA104305325_00455, SAMEA104305337_07638 Production host: Escherichia coli K-12 (bacteria) References: UniProt: V5VCK8, ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] #2: Chemical | ChemComp-M2K / | #3: Chemical | ChemComp-M2E / ( | #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.2 Å3/Da / Density % sol: 44.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 200mM Calcium Acetate, 20% PEG 3350 and 20% Glycerol (+ seed crystals) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Feb 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→71.342 Å / Num. obs: 37882 / % possible obs: 89.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 19.76 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.11 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.835→1.958 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1896 / CC1/2: 0.668 / Rrim(I) all: 0.793 / % possible all: 49 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1X07 Resolution: 1.84→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / SU R Cruickshank DPI: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.147 / SU Rfree Blow DPI: 0.131 / SU Rfree Cruickshank DPI: 0.129
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Displacement parameters | Biso max: 115.57 Å2 / Biso mean: 23.82 Å2 / Biso min: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.84→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.91 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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