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Yorodumi- PDB-6fqb: MurT/GatD peptidoglycan amidotransferase complex from Streptococc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fqb | ||||||
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Title | MurT/GatD peptidoglycan amidotransferase complex from Streptococcus pneumoniae R6 | ||||||
Components |
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Keywords | LIGASE / Mur family / amidotransferase / cytosolic | ||||||
Function / homology | Function and homology information lipid II isoglutaminyl synthase (glutamine-hydrolysing) / carbon-nitrogen ligase activity on lipid II / glutaminase / cobalamin biosynthetic process / glutaminase activity / glutamine metabolic process / ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape ...lipid II isoglutaminyl synthase (glutamine-hydrolysing) / carbon-nitrogen ligase activity on lipid II / glutaminase / cobalamin biosynthetic process / glutaminase activity / glutamine metabolic process / ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / transferase activity / zinc ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3 Å | ||||||
Authors | Morlot, C. / Contreras-Martel, C. / Leisico, F. / Straume, D. / Peters, K. / Hegnar, O.A. / Simon, N. / Villard, A.M. / Breukink, E. / Gravier-Pelletier, C. ...Morlot, C. / Contreras-Martel, C. / Leisico, F. / Straume, D. / Peters, K. / Hegnar, O.A. / Simon, N. / Villard, A.M. / Breukink, E. / Gravier-Pelletier, C. / Le Corre, L. / Vollmer, W. / Pietrancosta, N. / Havarstein, L.S. / Zapun, A. | ||||||
Funding support | France, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: Structure of the essential peptidoglycan amidotransferase MurT/GatD complex from Streptococcus pneumoniae. Authors: Morlot, C. / Straume, D. / Peters, K. / Hegnar, O.A. / Simon, N. / Villard, A.M. / Contreras-Martel, C. / Leisico, F. / Breukink, E. / Gravier-Pelletier, C. / Le Corre, L. / Vollmer, W. / ...Authors: Morlot, C. / Straume, D. / Peters, K. / Hegnar, O.A. / Simon, N. / Villard, A.M. / Contreras-Martel, C. / Leisico, F. / Breukink, E. / Gravier-Pelletier, C. / Le Corre, L. / Vollmer, W. / Pietrancosta, N. / Havarstein, L.S. / Zapun, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fqb.cif.gz | 486.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fqb.ent.gz | 409.8 KB | Display | PDB format |
PDBx/mmJSON format | 6fqb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/6fqb ftp://data.pdbj.org/pub/pdb/validation_reports/fq/6fqb | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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4 |
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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: 51940.234 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) Gene: A4260_05845, ERS019420_00606, ERS020535_00125, ERS021368_00525, ERS022199_00743, ERS043879_01366 Plasmid: pET30-HAT / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star References: UniProt: A0A0B7LND9, UniProt: Q8DNZ9*PLUS, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Protein | Mass: 29222.242 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) Gene: A4260_05840, AWW74_09320, CHL72_09035, CIT24_04835, CS877_04020, CSH34_00860, ERS003549_02292, ERS019166_00428, ERS019416_00232, ERS019420_00605, ERS019499_01955, ERS019595_01427, ERS020136_ ...Gene: A4260_05840, AWW74_09320, CHL72_09035, CIT24_04835, CS877_04020, CSH34_00860, ERS003549_02292, ERS019166_00428, ERS019416_00232, ERS019420_00605, ERS019499_01955, ERS019595_01427, ERS020136_01107, ERS020137_00292, ERS020140_00887, ERS020142_00808, ERS020143_01959, ERS020147_00746, ERS020148_00821, ERS020178_04008, ERS020408_00223, ERS020474_01302, ERS020521_00204, ERS020522_00778, ERS020523_00656, ERS020524_01042, ERS020526_00540, ERS020526_04035, ERS020527_01973, ERS020528_00148, ERS020541_00600, ERS020692_00332, ERS020827_01405, ERS020831_02169, ERS021300_01369, ERS021447_05442, ERS021629_07046, ERS021762_02260, ERS021858_02776, ERS022045_06260, ERS022071_00358, ERS022199_00742, ERS022232_05365, ERS022363_01901, ERS022390_00924, ERS044004_01668, ERS068943_01580, ERS232497_02277, ERS232498_04930, ERS232508_01880, ERS409064_00176, ERS558328_00424, SAMEA1026345_00620, SAMEA2626854_01213, SAMEA2626872_01126 Plasmid: pET30-HAT / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star References: UniProt: A0A062WUX3, UniProt: Q8DNZ8*PLUS, EC: 6.3.5.10 #3: Chemical | ChemComp-GLN / |
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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: 2.84 Å3/Da / Density % sol: 56.66 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 0.2 M tri-sodium citrate pH 6.1 14% PEG 3350 4 mM NiSO4 PH range: 6.0-6.2 |
-Data collection
Diffraction | Mean temperature: 193.15 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 28, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.965 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 68725 / % possible obs: 96.2 % / Redundancy: 3 % / Rsym value: 0.058 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 3→3.18 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 11055 / Rsym value: 0.447 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 22.948 / SU ML: 0.362 / Cross valid method: THROUGHOUT / ESU R Free: 0.405 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 86.337 Å2
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Refinement step | Cycle: 1 / Resolution: 3→50 Å
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Refine LS restraints |
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