+Open data
-Basic information
Entry | Database: PDB / ID: 4q6v | ||||||
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Title | LpoB C-terminal domain from Salmonella enterica (Sel-Met) | ||||||
Components | Penicillin-binding protein activator LpoB | ||||||
Keywords | PROTEIN BINDING / mixed alpha-beta / Lipoprotein / Activator of PBP1b / PBP1b / lipidation / outer-membrane | ||||||
Function / homology | Function and homology information periplasmic side of cell outer membrane / enzyme regulator activity / peptidoglycan biosynthetic process / regulation of cell shape Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.97 Å | ||||||
Authors | King, D.T. / Strynadka, N.C.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Structural Insights into the Lipoprotein Outer Membrane Regulator of Penicillin-binding Protein 1B. Authors: King, D.T. / Lameignere, E. / Strynadka, N.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q6v.cif.gz | 34 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q6v.ent.gz | 26.2 KB | Display | PDB format |
PDBx/mmJSON format | 4q6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4q6v_validation.pdf.gz | 423.7 KB | Display | wwPDB validaton report |
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Full document | 4q6v_full_validation.pdf.gz | 426.1 KB | Display | |
Data in XML | 4q6v_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 4q6v_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/4q6v ftp://data.pdbj.org/pub/pdb/validation_reports/q6/4q6v | HTTPS FTP |
-Related 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: 14594.638 Da / Num. of mol.: 1 / Fragment: LpoB C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: lpoB, STM1207 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZQ08 |
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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: 1.88 Å3/Da / Density % sol: 34.58 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1M NaAc pH4.6, 2M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9795 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 1, 2012 |
Radiation | Monochromator: KOHZU double crystal monochromator (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→49.3 Å / Num. all: 8231 / Num. obs: 8206 / % possible obs: 99.7 % |
Reflection shell | Resolution: 1.97→2.04 Å / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.97→49.3 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.885 / SU B: 6.773 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.211 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.992 Å2
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Refinement step | Cycle: LAST / Resolution: 1.97→49.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.974→2.025 Å / Total num. of bins used: 20
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