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Yorodumi- PDB-5lkw: Crystal structure of the peptidoglycan-associated lipoprotein (Pa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lkw | |||||||||
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Title | Crystal structure of the peptidoglycan-associated lipoprotein (Pal) from Burkholderia cepacia in complex with DAP | |||||||||
Components | Putative OmpA family lipoprotein | |||||||||
Keywords | MEMBRANE PROTEIN / DAP / Peptidoglycan-associated lipoprotein / Burkholderia cepacia complex (Bcc) | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Burkholderia cenocepacia (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Romano, M. / Ruggiero, A. / Berisio, R. | |||||||||
Citation | Journal: Cell. Microbiol. / Year: 2017 Title: The Burkholderia cenocepacia peptidoglycan-associated lipoprotein is involved in epithelial cell attachment and elicitation of inflammation. Authors: Dennehy, R. / Romano, M. / Ruggiero, A. / Mohamed, Y.F. / Dignam, S.L. / Mujica Troncoso, C. / Callaghan, M. / Valvano, M.A. / Berisio, R. / McClean, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lkw.cif.gz | 64.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lkw.ent.gz | 47 KB | Display | PDB format |
PDBx/mmJSON format | 5lkw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lk/5lkw ftp://data.pdbj.org/pub/pdb/validation_reports/lk/5lkw | HTTPS FTP |
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-Related structure data
Related structure data | 4b5cS S: Starting model for refinement |
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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
#1: Protein | Mass: 14907.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610) (bacteria) Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610 Gene: BCAL3204 / Production host: Escherichia coli (E. coli) / References: UniProt: B4EDC1 #2: Chemical | #3: 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: 2.26 Å3/Da / Density % sol: 45.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3350, 10mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 16690 / % possible obs: 100 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 1.6 / % possible all: 82.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4B5C Resolution: 2→14.69 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.89 / SU B: 4.613 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.4 Å2
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Refinement step | Cycle: 1 / Resolution: 2→14.69 Å
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