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Yorodumi- PDB-7u9k: Staphylococcus aureus D-alanine-D-alanine ligase in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7u9k | ||||||
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Title | Staphylococcus aureus D-alanine-D-alanine ligase in complex with ATP, D-ala-D-ala, Mg2+ and K+ | ||||||
Components |
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Keywords | LIGASE / ATP-grasp / nucleotide binding / metal binding | ||||||
Function / homology | Function and homology information D-alanine-D-alanine ligase / D-alanine-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Pederick, J.L. / Bruning, J.B. | ||||||
Funding support | 1items
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Citation | Journal: Bioorg.Med.Chem. / Year: 2023 Title: Structure-guided design and synthesis of ATP-competitive N-acyl-substituted sulfamide d-alanine-d-alanine ligase inhibitors. Authors: Becker, R. / Pederick, J.L. / Dawes, E.G. / Bruning, J.B. / Abell, A.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7u9k.cif.gz | 153.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u9k.ent.gz | 115.5 KB | Display | PDB format |
PDBx/mmJSON format | 7u9k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/7u9k ftp://data.pdbj.org/pub/pdb/validation_reports/u9/7u9k | HTTPS FTP |
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-Related structure data
Related structure data | 2i87S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Polypeptide(D) , 2 types, 3 molecules ABF
#1: Protein | Mass: 41348.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Strain: NCTC 8325 / PS 47 / Gene: ddl, SAOUHSC_02318 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2FWH3, D-alanine-D-alanine ligase #2: Polypeptide(D) | | Mass: 160.171 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: D-alanine-D-alanine dipeptide product formed by D-alanine-D-alanine ligase Source: (synth.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) |
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-Non-polymers , 5 types, 290 molecules
#3: Chemical | ChemComp-K / #4: Chemical | #5: Chemical | ChemComp-ADP / | #6: Chemical | ChemComp-ATP / | #7: 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: 1.98 Å3/Da / Density % sol: 37.95 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 20 - 30% PEG 3350, 0.5 M KCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 14, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2→38.02 Å / Num. obs: 43862 / % possible obs: 99.8 % / Redundancy: 6.6 % / CC1/2: 0.989 / Rmerge(I) obs: 0.216 / Rpim(I) all: 0.093 / Rrim(I) all: 0.236 / Net I/σ(I): 9.3 / Num. measured all: 289114 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2I87 Resolution: 2→37.68 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 30.05 / 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: 74.29 Å2 / Biso mean: 32.1961 Å2 / Biso min: 10.28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→37.68 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15
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