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- PDB-7osq: Crystal structure of UDP-N-acetylenolpyruvoylglucosamine reductas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7osq | ||||||
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Title | Crystal structure of UDP-N-acetylenolpyruvoylglucosamine reductase (MurB) from Pseudomonas aeruginosa in complex with FAD and a pyrazole derivative (fragment 18) | ||||||
![]() | UDP-N-acetylenolpyruvoylglucosamine reductase | ||||||
![]() | OXIDOREDUCTASE / Peptidoglycan-biosynthesis / Fragment based drug discovery | ||||||
Function / homology | ![]() UDP-N-acetylmuramate dehydrogenase / UDP-N-acetylmuramate dehydrogenase activity / peptidoglycan biosynthetic process / FAD binding / cell wall organization / flavin adenine dinucleotide binding / regulation of cell shape / cell division / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Acebron-Garcia de Eulate, M. / Mayol-Llinas, J. / Blundell, T.L. / Kim, S.Y. / Mendes, V. / Abell, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery of Novel Inhibitors of Uridine Diphosphate- N -Acetylenolpyruvylglucosamine Reductase (MurB) from Pseudomonas aeruginosa , an Opportunistic Infectious Agent Causing Death in Cystic Fibrosis Patients. Authors: Acebron-Garcia-de-Eulate, M. / Mayol-Llinas, J. / Holland, M.T.O. / Kim, S.Y. / Brown, K.P. / Marchetti, C. / Hess, J. / Di Pietro, O. / Mendes, V. / Abell, C. / Floto, R.A. / Coyne, A.G. / Blundell, T.L. #1: ![]() Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175.4 KB | Display | ![]() |
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PDB format | ![]() | 114.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 21 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7or2C ![]() 7orzC ![]() 4jb1S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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: 37678.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: murB, PA2977 / Production host: ![]() ![]() References: UniProt: Q9HZM7, UDP-N-acetylmuramate dehydrogenase |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-0JI / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.92 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 30% glycerol and 22% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96861 Å / Relative weight: 1 |
Reflection | Resolution: 2.06693→75.908 Å / Num. obs: 27031 / % possible obs: 99.89 % / Redundancy: 20 % / Biso Wilson estimate: 30.4 Å2 / CC1/2: 0.99 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.067→2.103 Å / Mean I/σ(I) obs: 1.5 / Num. measured obs: 27421 / Num. unique obs: 2183 / CC1/2: 0.352 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4JB1 Resolution: 2.07→40.21 Å / SU ML: 0.2324 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.0181 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 43.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.07→40.21 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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