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Yorodumi- PDB-3pmd: Crystal structure of the sporulation inhibitor pXO1-118 from Baci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pmd | ||||||
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Title | Crystal structure of the sporulation inhibitor pXO1-118 from Bacillus anthracis | ||||||
Components | Conserved domain protein | ||||||
Keywords | LIPID BINDING PROTEIN / globin fold / non-heme globin / sporulation / Bacillus anthracis / kinase sensor domain / chloride coordination / fatty acid-binding protein | ||||||
Function / homology | Histidine kinase N-terminal domain / Histidine kinase, N-terminal / : / Histidine kinase N terminal / Globin-like / Orthogonal Bundle / Mainly Alpha / UNDECANOIC ACID / Conserved domain protein Function and homology information | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å | ||||||
Authors | Stranzl, G.R. / Santelli, E. / Bankston, L.A. / La Clair, C. / Bobkov, A. / Schwarzenbacher, R. / Godzik, A. / Perego, M. / Grynberg, M. / Liddington, R.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structural Insights into Inhibition of Bacillus anthracis Sporulation by a Novel Class of Non-heme Globin Sensor Domains. Authors: Stranzl, G.R. / Santelli, E. / Bankston, L.A. / La Clair, C. / Bobkov, A. / Schwarzenbacher, R. / Godzik, A. / Perego, M. / Grynberg, M. / Liddington, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pmd.cif.gz | 81.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pmd.ent.gz | 61.8 KB | Display | PDB format |
PDBx/mmJSON format | 3pmd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pmd_validation.pdf.gz | 426 KB | Display | wwPDB validaton report |
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Full document | 3pmd_full_validation.pdf.gz | 426.7 KB | Display | |
Data in XML | 3pmd_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 3pmd_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/3pmd ftp://data.pdbj.org/pub/pdb/validation_reports/pm/3pmd | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 18540.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: GBAA_pXO1_0148, pX01-118 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q44635 |
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#2: Chemical | ChemComp-11A / |
#3: Chemical | ChemComp-CL / |
#4: 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: 2.22 Å3/Da / Density % sol: 44.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 5.4 Details: 5% PEG1000, 40% PEG400, 0.1 M TrisHCl, pH 5.4, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9781 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 13, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9781 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→50 Å / Num. obs: 16351 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.038 / Net I/σ(I): 55.1 |
Reflection shell | Resolution: 1.76→1.82 Å / Rmerge(I) obs: 0.276 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.76→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.063 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.122 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.056 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.762→1.807 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -8.038 Å / Origin y: 32.5633 Å / Origin z: 13.4902 Å
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