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- PDB-7ti7: Crystal Structure of UDP-N-acetylmuramoylalanine-D-glutamate liga... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ti7 | ||||||
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Title | Crystal Structure of UDP-N-acetylmuramoylalanine-D-glutamate ligase from Acinetobacter baumannii AB5075-UW in complex with ADP | ||||||
![]() | UDP-N-acetylmuramoylalanine--D-glutamate ligase | ||||||
![]() | LIGASE / SSGCID / MurD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
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 / 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 UDP-N-acetylmuramoylalanine-D-glutamate ligase from Acinetobacter baumannii AB5075-UW in complex with ADP Authors: Abendroth, J. / DeBouver, N.D. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 239.4 KB | Display | ![]() |
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PDB format | ![]() | 155 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 850.7 KB | Display | ![]() |
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Full document | ![]() | 853.8 KB | Display | |
Data in XML | ![]() | 23.5 KB | Display | |
Data in CIF | ![]() | 36.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7sirS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 49059.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: murD, Aba9201_12330, ABUW_3630, APC21_11165, C6N18_02095, EA686_02860, EGM95_19310, F2P40_16560, GNY86_17350, NCTC13421_03598, SI89_12870 Plasmid: AcbaC.17938.a.B1 / Production host: ![]() ![]() References: UniProt: A0A0B9W6J3, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase |
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-Non-polymers , 6 types, 552 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ADP / | ||||||
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#3: Chemical | ChemComp-MG / | ||||||
#4: Chemical | #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-CA / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.8 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Molecular Dimensions Morpheus screen condition a6: 10% (w/V) PEG 8000, 20% (V/V) ethylene gycol: 30mM magnesium chloride and calcium chloride: 100mM MOPS / HEPES pH 7.5: AcbaC.17938.a.B1. ...Details: Molecular Dimensions Morpheus screen condition a6: 10% (w/V) PEG 8000, 20% (V/V) ethylene gycol: 30mM magnesium chloride and calcium chloride: 100mM MOPS / HEPES pH 7.5: AcbaC.17938.a.B1.PS02380: tray 323738a6: cryo: direct: puck: loi2-1 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Dec 9, 2021 / Details: Beryllium Lenses | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→50 Å / Num. obs: 86055 / % possible obs: 100 % / Redundancy: 8.094 % / Biso Wilson estimate: 27.158 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.066 / Χ2: 0.944 / Net I/σ(I): 19.03 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: apo structure, pdb entry 7SIR Resolution: 1.5→45.91 Å / SU ML: 0.1468 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.388 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: 31.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→45.91 Å
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Refine LS restraints |
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LS refinement shell |
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