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- PDB-8v8y: Crystal Structure of Apo UDP-N-acetylmuramoylalanine--D-glutamate... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8v8y | |||||||||
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Title | Crystal Structure of Apo UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli (Orthorhombic P form) | |||||||||
![]() | UDP-N-acetylmuramoylalanine--D-glutamate ligase | |||||||||
![]() | LIGASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / MurD | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of Apo UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli (Orthorhombic P form) Authors: Seibold, S. / Lovell, S. / Battaile, K.P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 188.5 KB | Display | ![]() |
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PDB format | ![]() | 144.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.1 KB | Display | ![]() |
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Full document | ![]() | 448.1 KB | Display | |
Data in XML | ![]() | 20.1 KB | Display | |
Data in CIF | ![]() | 30.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 49352.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P14900, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase |
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-Non-polymers , 6 types, 323 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NA / | ||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-MPD / ( | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.45 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Morpheus A8: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM HEPES/MOPS, pH 7.5, 30 mM MgCl2 and 30 mM CaCl2. EscoA.17938.a.A1.PW39141 at 22.4 mg/mL. Inhibitor added but not ...Details: Morpheus A8: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM HEPES/MOPS, pH 7.5, 30 mM MgCl2 and 30 mM CaCl2. EscoA.17938.a.A1.PW39141 at 22.4 mg/mL. Inhibitor added but not bound. plate 13506 well A8 drop 1. Puck: PSL-1803, Cryo: direct |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 8, 2023 |
Radiation | Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→44.36 Å / Num. obs: 47702 / % possible obs: 97.6 % / Redundancy: 5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.034 / Rrim(I) all: 0.077 / Χ2: 0.98 / Net I/σ(I): 12.7 / Num. measured all: 236458 |
Reflection shell | Resolution: 1.65→1.68 Å / % possible obs: 96.2 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.797 / Num. measured all: 12233 / Num. unique obs: 2372 / CC1/2: 0.764 / Rpim(I) all: 0.383 / Rrim(I) all: 0.886 / Χ2: 1.04 / Net I/σ(I) obs: 2 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 1.65→40.58 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 |
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