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Yorodumi- PDB-9bn8: Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate lig... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9bn8 | |||||||||
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Title | Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli in complex with UMA and inhibitor A19 | |||||||||
Components | UDP-N-acetylmuramoylalanine--D-glutamate ligase | |||||||||
Keywords | LIGASE/LIGASE INHIBITOR / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / MurD / LIGASE / LIGASE-LIGASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase / UDP-N-acetylmuramoylalanine-D-glutamate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / ATP binding / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | |||||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | United States, 2items
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Citation | Journal: To be published Title: Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli in complex with UMA and inhibitor A19 Authors: Liu, L. / Seibold, S. / Lovell, S. / Battaile, K.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9bn8.cif.gz | 202.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9bn8.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9bn8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/9bn8 ftp://data.pdbj.org/pub/pdb/validation_reports/bn/9bn8 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 47906.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: murD / Plasmid: EscoA.17938.a.AE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P14900 |
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-Non-polymers , 5 types, 518 molecules
#2: Chemical | ChemComp-UMA / | ||||
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#3: Chemical | ChemComp-A1AQS / Mass: 300.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12N6OS / Feature type: SUBJECT OF INVESTIGATION | ||||
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
-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: 3.02 Å3/Da / Density % sol: 59.22 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.9M ammonium sulfate, 7% (v/v) PEG 400, 0.1M Hepes 7.5. EscoA.17938.a.AE1.PW39153 at 17.4 mg/mL. Soaked with 2mM A19 in crystallant (10 ul) for 2h, and transferred to another 10 ul of the ...Details: 1.9M ammonium sulfate, 7% (v/v) PEG 400, 0.1M Hepes 7.5. EscoA.17938.a.AE1.PW39153 at 17.4 mg/mL. Soaked with 2mM A19 in crystallant (10 ul) for 2h, and transferred to another 10 ul of the same solution for another 2h. plate Liu-Lim-116 A2. Puck: PSL-0401, Cryo: 2.5M Lithium Sulfate + 2mM inhibitor A19 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Apr 13, 2024 |
Radiation | Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→67.38 Å / Num. obs: 124023 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 1 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.019 / Rrim(I) all: 0.072 / Χ2: 0.99 / Net I/σ(I): 17.7 / Num. measured all: 1676743 |
Reflection shell | Resolution: 1.35→1.39 Å / % possible obs: 100 % / Redundancy: 10 % / Rmerge(I) obs: 1.317 / Num. measured all: 91897 / Num. unique obs: 9171 / CC1/2: 0.682 / Rpim(I) all: 0.435 / Rrim(I) all: 1.388 / Χ2: 1.01 / Net I/σ(I) obs: 1.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→58.9 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→58.9 Å
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Refine LS restraints |
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LS refinement shell |
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