+Open data
-Basic information
Entry | Database: PDB / ID: 6dr3 | ||||||
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Title | Crystal structure of E. coli LpoA amino terminal domain | ||||||
Components | Penicillin-binding protein activator LpoA | ||||||
Keywords | BIOSYNTHETIC PROTEIN / TPR-like motifs OUTER MEMBRANE LIPOPROTEIN ACTIVATOR OF PBP1A PEPTIDOGLYCAN | ||||||
Function / homology | Function and homology information periplasmic side of cell outer membrane / hydrolase activity, hydrolyzing O-glycosyl compounds / enzyme regulator activity / peptidoglycan biosynthetic process / cell outer membrane / regulation of cell shape / periplasmic space / enzyme binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.101 Å | ||||||
Authors | Kelley, A.C. / Saper, M.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2019 Title: Crystal structures of the amino-terminal domain of LpoA from Escherichia coli and Haemophilus influenzae. Authors: Kelley, A. / Vijayalakshmi, J. / Saper, M.A. #1: Journal: J. Biol. Chem. / Year: 2017 Title: Structural analyses of the Haemophilus influenzae peptidoglycan synthase activator LpoA suggest multiple conformations in solution. Authors: Sathiyamoorthy, K. / Vijayalakshmi, J. / Tirupati, B. / Fan, L. / Saper, M.A. #2: Journal: Structure / Year: 2014 Title: Elongated structure of the outer-membrane activator of peptidoglycan synthesis LpoA: implications for PBP1A stimulation. Authors: Jean, N.L. / Bougault, C.M. / Lodge, A. / Derouaux, A. / Callens, G. / Egan, A.J. / Ayala, I. / Lewis, R.J. / Vollmer, W. / Simorre, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dr3.cif.gz | 144.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dr3.ent.gz | 115 KB | Display | PDB format |
PDBx/mmJSON format | 6dr3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dr3_validation.pdf.gz | 419 KB | Display | wwPDB validaton report |
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Full document | 6dr3_full_validation.pdf.gz | 420.2 KB | Display | |
Data in XML | 6dr3_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 6dr3_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/6dr3 ftp://data.pdbj.org/pub/pdb/validation_reports/dr/6dr3 | HTTPS FTP |
-Related structure data
Related structure data | 6dcjC 4p29S 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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Unit cell |
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-Components
#1: Protein | Mass: 25178.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: lpoA, yraM, b3147, JW3116 / Plasmid: pMCSG7-EcLpoA-N(31-252) Details (production host): Expresses of fusion of His6, TeV cleavage sequence, and EcLpoA-N(31-252) Cell line (production host): Origami 2(DE3) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): Origami 2(DE3) / Variant (production host): Origami 2(DE3) / References: UniProt: P45464 |
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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: 2.38 Å3/Da / Density % sol: 48.3 % / Description: needles with square cross-section |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Drops contained 0.5 ul protein and 0.5 ul precipitant and equilibrated against precipitant by vapor diffusion. Protein: 19 mg/ml in 50 mM NaCl, 1 mM dithiothreitol, 50 mM TrisHCl pH 7.5. ...Details: Drops contained 0.5 ul protein and 0.5 ul precipitant and equilibrated against precipitant by vapor diffusion. Protein: 19 mg/ml in 50 mM NaCl, 1 mM dithiothreitol, 50 mM TrisHCl pH 7.5. Precipitant contained: 0.03 M magnesium chloride hexahydrate, 0.03 M calcium chloride dihydrate, 5% glycerol, 0.1 M Buffer System 1, pH 6.5, 10% PEG 20,000, 17% PEG 550 MME Buffer System 1: 30 mL MES (pH 3.11) was titrated with 24.1 mL Imidazole (pH 10.23) to a final pH of 6.5 |
-Data collection
Diffraction | Mean temperature: 140 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97717 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 2, 2017 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97717 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→30 Å / Num. obs: 14791 / % possible obs: 99.8 % / Redundancy: 10.9 % / Biso Wilson estimate: 27.23 Å2 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.032 / Rrim(I) all: 0.109 / Χ2: 0.959 / Net I/σ(I): 6.7 / Num. measured all: 160798 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4P29 Resolution: 2.101→22.697 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.47 / Phase error: 20.19
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 158.63 Å2 / Biso mean: 42.4992 Å2 / Biso min: 14.45 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.101→22.697 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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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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