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Yorodumi- PDB-6h5e: Crystal Structure of the GatD/MurT Enzyme Complex from Staphyloco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h5e | |||||||||
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Title | Crystal Structure of the GatD/MurT Enzyme Complex from Staphylococcus aureus with bound AMPPNP | |||||||||
Components |
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Keywords | BIOSYNTHETIC PROTEIN / cell wall biosynthesis / peptidoglycan / antibiotic resistance | |||||||||
Function / homology | Function and homology information 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 | Staphylococcus aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.139 Å | |||||||||
Authors | Noeldeke, E.R. / Niemann, V. / Stoerk, E. / Stehle, T. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Sci Rep / Year: 2018 Title: Structural basis of cell wall peptidoglycan amidation by the GatD/MurT complex of Staphylococcus aureus. Authors: Noldeke, E.R. / Muckenfuss, L.M. / Niemann, V. / Muller, A. / Stork, E. / Zocher, G. / Schneider, T. / Stehle, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6h5e.cif.gz | 518.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h5e.ent.gz | 424.7 KB | Display | PDB format |
PDBx/mmJSON format | 6h5e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/6h5e ftp://data.pdbj.org/pub/pdb/validation_reports/h5/6h5e | HTTPS FTP |
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-Related structure data
Related structure data | 6gs2SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 28539.184 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: N315 / Gene: SA1707 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3JN63 #2: Protein | Mass: 49250.883 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: BTN44_02275, C3B39_12565, EP54_01845, EQ90_00760, HMPREF3211_01062 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D6HDA2, UniProt: A0A0H3JUU7*PLUS |
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-Non-polymers , 7 types, 387 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-144 / | #7: Chemical | ChemComp-GOL / #8: Chemical | #9: Water | ChemComp-HOH / | |
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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: 2.57 Å3/Da / Density % sol: 52.21 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9.1 Details: 100 mM Tris pH 9.1 350 mM MgCl2 18 % PEG 8000 13 % Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.139→50 Å / Num. obs: 82581 / % possible obs: 99.8 % / Redundancy: 13.5 % / Biso Wilson estimate: 51.9 Å2 / CC1/2: 1 / Rpim(I) all: 0.031 / Rrim(I) all: 0.116 / Net I/av σ(I): 19.36 / Net I/σ(I): 19.37 |
Reflection shell | Resolution: 2.139→2.216 Å / Redundancy: 12.6 % / Mean I/σ(I) obs: 1.23 / Num. unique obs: 8030 / CC1/2: 0.847 / Rpim(I) all: 0.661 / Rrim(I) all: 2.369 / % possible all: 97.95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GS2 Resolution: 2.139→49.075 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.32
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.139→49.075 Å
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Refine LS restraints |
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LS refinement shell |
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