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Yorodumi- PDB-5kcn: Crystal Structure of full-length LpoA from Haemophilus influenzae... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kcn | |||||||||
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Title | Crystal Structure of full-length LpoA from Haemophilus influenzae at 1.97 angstrom resolution | |||||||||
Components | Penicillin-binding protein activator LpoA | |||||||||
Keywords | BIOSYNTHETIC PROTEIN / Outer membrane lipoprotein / PBP1A / transpeptidase. peptidoglycan | |||||||||
Function / homology | Penicillin-binding protein activator LpoA / LppC putative lipoprotein / periplasmic side of cell outer membrane / enzyme regulator activity / peptidoglycan biosynthetic process / Periplasmic binding protein-like I / Tetratricopeptide-like helical domain superfamily / regulation of cell shape / Penicillin-binding protein activator LpoA Function and homology information | |||||||||
Biological species | Haemophilus influenzae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.965 Å | |||||||||
Authors | Sathiyamoorthy, K. / Saper, M.A. | |||||||||
Funding support | United States, 2items
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Citation | 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. #1: Journal: Proteins / Year: 2008 Title: Structure of YraM, a protein essential for growth of Haemophilus influenzae. Authors: Vijayalakshmi, J. / Akerley, B.J. / Saper, M.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kcn.cif.gz | 322.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kcn.ent.gz | 264.8 KB | Display | PDB format |
PDBx/mmJSON format | 5kcn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kcn_validation.pdf.gz | 421 KB | Display | wwPDB validaton report |
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Full document | 5kcn_full_validation.pdf.gz | 426.8 KB | Display | |
Data in XML | 5kcn_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 5kcn_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/5kcn ftp://data.pdbj.org/pub/pdb/validation_reports/kc/5kcn | HTTPS FTP |
-Related structure data
Related structure data | 4p29SC 5vatC 5vbgC 3ckmS 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: 60010.074 Da / Num. of mol.: 1 / Fragment: UNP residues 33-575 Source method: isolated from a genetically manipulated source Details: LpoA residues 33-575 / Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: lpoA, HI_1655 / Plasmid: pETBlue-2 / Details (production host): T7 promoter / Production host: Escherichia coli (E. coli) / Strain (production host): Origami(DE3)/pLacI / References: UniProt: P45299 |
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#2: Chemical | ChemComp-CL / |
#3: 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: 2.4 Å3/Da / Density % sol: 48.79 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 1 microliter of concentrated protein (33 mg/ml in 150 mM NaCl, 50 mM Tris-HCl, pH 8.0) and 1 microliter precipitant [25% w/v PEG 1500, 0.1 M MMT buffer (20 mM DL-malic acid, 40 mM MES, 40 mM ...Details: 1 microliter of concentrated protein (33 mg/ml in 150 mM NaCl, 50 mM Tris-HCl, pH 8.0) and 1 microliter precipitant [25% w/v PEG 1500, 0.1 M MMT buffer (20 mM DL-malic acid, 40 mM MES, 40 mM Tris-HCl), pH 4.0] and 0.2 microliter 30% xylitol Temp details: 277 for 2 days, then 295 |
-Data collection
Diffraction | Mean temperature: 125 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 13, 2009 / Details: Monochromator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: 0.9786 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.965→50 Å / Num. obs: 42000 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 31.05 Å2 / Rmerge(I) obs: 0.058 / Net I/av σ(I): 29.518 / Net I/σ(I): 21.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4P29 and 3CKM Resolution: 1.965→31.783 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.72 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.965→31.783 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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