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- PDB-7q8e: Crystal Structure of the MurT-GatD Enzyme Complex from Staphyloco... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7q8e | |||||||||||||||
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Title | Crystal Structure of the MurT-GatD Enzyme Complex from Staphylococcus aureus COL strain | |||||||||||||||
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![]() | LIGASE / Essential Glutamine Amidotransferase / Glutaminase/Ligase / Bacterial Peptidoglycan Amidation. | |||||||||||||||
Function / homology | ![]() lipid II isoglutaminyl synthase (glutamine-hydrolysing) / carbon-nitrogen ligase activity on lipid II / acid-amino acid ligase activity / glutaminase / cobalamin biosynthetic process / glutaminase activity / glutamine metabolic process / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape ...lipid II isoglutaminyl synthase (glutamine-hydrolysing) / carbon-nitrogen ligase activity on lipid II / acid-amino acid ligase activity / glutaminase / cobalamin biosynthetic process / glutaminase activity / glutamine metabolic process / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / zinc ion binding / ATP binding Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Leisico, F. / Romao, M.J. / Santos-Silva, T. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of the MurT-GatD Enzyme Complex from Staphylococcus aureus COL strain Authors: Leisico, F. / Romao, M.J. / Santos-Silva, T. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 611.1 KB | Display | ![]() |
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PDB format | ![]() | 423.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 922 KB | Display | ![]() |
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Full document | ![]() | 929.5 KB | Display | |
Data in XML | ![]() | 43.5 KB | Display | |
Data in CIF | ![]() | 59.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gs2S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: Protein | Mass: 49264.910 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: murT, SACOL1951 / Production host: ![]() ![]() References: UniProt: A0A0H2WZQ7, lipid II isoglutaminyl synthase (glutamine-hydrolysing) #2: Protein | Mass: 28539.184 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: gatD, SACOL1950 / Production host: ![]() ![]() References: UniProt: A0A0H2WZ38, lipid II isoglutaminyl synthase (glutamine-hydrolysing), glutaminase #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 42.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 30 % (w/v) PEG 4,000, 100 mM Tris-HCl pH 8.5 and 200 mM MgCl2; |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→49.31 Å / Num. obs: 30388 / % possible obs: 99.99 % / Redundancy: 6.9 % / Biso Wilson estimate: 62.9479579287 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.113 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 17 / Num. unique obs: 4366 / CC1/2: 0.58 / Rpim(I) all: 0.696 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6GS2 Resolution: 2.90001720351→49.3089437971 Å / SU ML: 0.442344360262 / Cross valid method: FREE R-VALUE / σ(F): 1.33648315019 / Phase error: 30.4477447237 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: 73.5780373074 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.90001720351→49.3089437971 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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