+Open data
-Basic information
Entry | Database: PDB / ID: 6snr | ||||||||||||
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Title | Crystal structure of FemX | ||||||||||||
Components | Lipid II:glycine glycyltransferase | ||||||||||||
Keywords | ANTIMICROBIAL PROTEIN / Antibiotics / Factors essential for meticillin resistance proteins (Fem proteins) / Fem ligases / Staphylococcus aureus / FemX / Enzymes involved in cross-bridge formation | ||||||||||||
Function / homology | Function and homology information lipid II:glycine glycyltransferase / aminoacyltransferase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.62 Å | ||||||||||||
Authors | Fulop, V. / Hinxman, K. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Structure / Year: 2021 Title: Structure-based modeling and dynamics of MurM, a Streptococcus pneumoniae penicillin resistance determinant present at the cytoplasmic membrane. Authors: York, A. / Lloyd, A.J. / Del Genio, C.I. / Shearer, J. / Hinxman, K.J. / Fritz, K. / Fulop, V. / Dowson, C.G. / Khalid, S. / Roper, D.I. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6snr.cif.gz | 93.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6snr.ent.gz | 73.7 KB | Display | PDB format |
PDBx/mmJSON format | 6snr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sn/6snr ftp://data.pdbj.org/pub/pdb/validation_reports/sn/6snr | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 48487.199 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: femX, fmhB / Production host: Escherichia coli (E. coli) References: UniProt: P0C1Q0, lipid II:glycine glycyltransferase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.6 % / Description: Needle |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6.3 Details: 0.12 M Ethylene Glycol, 0.1 M MES/imidazole pH 6.3 and 28 % Ethylene Glycol-PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 4, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→53 Å / Num. obs: 65058 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.031 / Rrim(I) all: 0.078 / Rsym value: 0.065 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.62→1.66 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4782 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.62→52.27 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.929 / SU B: 1.711 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.092 / 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: 26.241 Å2
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Refinement step | Cycle: 1 / Resolution: 1.62→52.27 Å
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Refine LS restraints |
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