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Yorodumi- PDB-3t95: Crystal structure of LsrB from Yersinia pestis complexed with aut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t95 | |||||||||
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Title | Crystal structure of LsrB from Yersinia pestis complexed with autoinducer-2 | |||||||||
Components | Autoinducer 2-binding protein lsrB | |||||||||
Keywords | SIGNALING PROTEIN / periplasmic binding protein fold / periplasmic space | |||||||||
Function / homology | Function and homology information ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space / carbohydrate binding Similarity search - Function | |||||||||
Biological species | Yersinia pestis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||
Authors | Kavanaugh, J.S. / Gakhar, L. / Horswill, A.R. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: The structure of LsrB from Yersinia pestis complexed with autoinducer-2. Authors: Kavanaugh, J.S. / Gakhar, L. / Horswill, A.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t95.cif.gz | 85 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t95.ent.gz | 61.5 KB | Display | PDB format |
PDBx/mmJSON format | 3t95.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t95_validation.pdf.gz | 440.4 KB | Display | wwPDB validaton report |
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Full document | 3t95_full_validation.pdf.gz | 441.1 KB | Display | |
Data in XML | 3t95_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 3t95_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t9/3t95 ftp://data.pdbj.org/pub/pdb/validation_reports/t9/3t95 | HTTPS FTP |
-Related structure data
Related structure data | 1tjyS 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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Unit cell |
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-Components
#1: Protein | Mass: 36353.074 Da / Num. of mol.: 1 / Fragment: UNP residues 26-339 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: lsrB, y3772, YPO0409, YP_3772 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q74PW2 |
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#2: Sugar | ChemComp-PAV / ( |
#3: Water | ChemComp-HOH / |
Nonpolymer details | LIGAND PAV (AUTOINDUCER-2) WAS SYNTHESIZED FROM S-ADENOSYLHOMOCYSTEINE USING PURIFIED PFS ...LIGAND PAV (AUTOINDUCE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Qiagen PEG Suite condition number 92: 20% PEG3350, 200 mM di-ammonium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 25, 2008 / Details: Osmic Blue |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→62.62 Å / Num. all: 31947 / Num. obs: 31947 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 6.5 / Num. unique all: 4339 / % possible all: 93.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TJY Resolution: 1.75→19.749 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.244 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 17.389 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→19.749 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
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