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Yorodumi- PDB-7k9a: Crystal Structure of P. aeruginosa LpxC with N-Hydroxyformamide i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7k9a | ||||||
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Title | Crystal Structure of P. aeruginosa LpxC with N-Hydroxyformamide inhibitor | ||||||
Components | UDP-3-O-acyl-N-acetylglucosamine deacetylase | ||||||
Keywords | HYDROLASE / LpxC | ||||||
Function / homology | Function and homology information UDP-3-O-acyl-N-acetylglucosamine deacetylase / UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity / UDP-3-O-acyl-N-acetylglucosamine deacetylase activity / lipid A biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Sacco, M. / Chen, Y. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2020 Title: N-Hydroxyformamide LpxC inhibitors, their in vivo efficacy in a mouse Escherichia coli infection model, and their safety in a rat hemodynamic assay. Authors: Furuya, T. / Shapiro, A.B. / Comita-Prevoir, J. / Kuenstner, E.J. / Zhang, J. / Ribe, S.D. / Chen, A. / Hines, D. / Moussa, S.H. / Carter, N.M. / Sylvester, M.A. / Romero, J.A.C. / Vega, C.V. ...Authors: Furuya, T. / Shapiro, A.B. / Comita-Prevoir, J. / Kuenstner, E.J. / Zhang, J. / Ribe, S.D. / Chen, A. / Hines, D. / Moussa, S.H. / Carter, N.M. / Sylvester, M.A. / Romero, J.A.C. / Vega, C.V. / Sacco, M.D. / Chen, Y. / O'Donnell, J.P. / Durand-Reville, T.F. / Miller, A.A. / Tommasi, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7k9a.cif.gz | 140.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7k9a.ent.gz | 107.3 KB | Display | PDB format |
PDBx/mmJSON format | 7k9a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7k9a_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7k9a_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7k9a_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | 7k9a_validation.cif.gz | 37.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/7k9a ftp://data.pdbj.org/pub/pdb/validation_reports/k9/7k9a | HTTPS FTP |
-Related structure data
Related structure data | 7k99C 5u39S 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AC
#1: Protein | Mass: 33475.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: lpxC, envA, PA4406 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P47205, UDP-3-O-acyl-N-acetylglucosamine deacetylase |
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-Non-polymers , 7 types, 263 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-DMS / | #6: Chemical | #7: Chemical | ChemComp-W8P / | #8: Water | ChemComp-HOH / | |
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-Details
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 Å3/Da / Density % sol: 38.58 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.6 M AmSO4, 0.5 M LiCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 25, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 34441 / % possible obs: 97.6 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.057 / Rrim(I) all: 0.13 / Χ2: 1.225 / Net I/σ(I): 5.2 / Num. measured all: 161786 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5u39 Resolution: 2→47.89 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.545 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.05 Å2 / Biso mean: 31.885 Å2 / Biso min: 6.24 Å2
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Refinement step | Cycle: final / Resolution: 2→47.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.003→2.055 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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