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Yorodumi- PDB-2xtw: Structure of QnrB1 (Full length), a plasmid-mediated fluoroquinol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xtw | ||||||
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Title | Structure of QnrB1 (Full length), a plasmid-mediated fluoroquinolone resistance protein | ||||||
Components | QNRB1 | ||||||
Keywords | CELL CYCLE / PENTAPEPTIDE REPEAT / PRP / ANTIBIOTIC RESISTANCE / RIGHT HANDED QUADRILATERAL BETA-HELIX | ||||||
Function / homology | E3 ubiquitin-protein ligase SopA / Pentapeptide repeats (9 copies) / Pentapeptide repeat / Pectate Lyase C-like / 3 Solenoid / Mainly Beta / QnrB1 Function and homology information | ||||||
Biological species | KLEBSIELLA PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.803 Å | ||||||
Authors | Vetting, M.W. / Hegde, S.S. / Park, C.H. / Jacoby, G.A. / Hooper, D.C. / Blanchard, J.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structure of Qnrb1, a Plasmid-Mediated Fluoroquinolone Resistance Factor. Authors: Vetting, M.W. / Hegde, S.S. / Wang, M. / Jacoby, G.A. / Hooper, D.C. / Blanchard, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xtw.cif.gz | 166.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xtw.ent.gz | 134.9 KB | Display | PDB format |
PDBx/mmJSON format | 2xtw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xtw_validation.pdf.gz | 445.4 KB | Display | wwPDB validaton report |
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Full document | 2xtw_full_validation.pdf.gz | 461.9 KB | Display | |
Data in XML | 2xtw_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 2xtw_validation.cif.gz | 41 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/2xtw ftp://data.pdbj.org/pub/pdb/validation_reports/xt/2xtw | HTTPS FTP |
-Related 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: 24126.078 Da / Num. of mol.: 4 Fragment: TOPISOMERASE POISON RESISTANCE FACTOR, RESIDUES 13-226 Source method: isolated from a genetically manipulated source Source: (gene. exp.) KLEBSIELLA PNEUMONIAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2I1Y8 Sequence details | CLONED INTO A CLEAVABLE PET28 VECTOR WITH CLEAVABLE HIS6 TAG. PROTEIN IS CLEAVED LEAVING GSH ON N ...CLONED INTO A CLEAVABLE PET28 VECTOR WITH CLEAVABLE HIS6 TAG. PROTEIN IS CLEAVED LEAVING GSH ON N TERMINUS. PROTEIN WAS CLONED STARTING FROM 2ND MET OF THE GENBANK SEQUENCE. | |
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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: 2.73 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | Temperature: 277 K / pH: 4.5 Details: 100 MM NA/K PHOSPHATE PH 4.5, 2 M NACL AT 4 DEGREES C |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→40 Å / Num. obs: 26120 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 39.58 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 6.5 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.803→47.268 Å / SU ML: 0.43 / σ(F): 0 / Phase error: 35.02 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.22 Å2 / ksol: 0.366 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.1 Å2
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Refinement step | Cycle: LAST / Resolution: 2.803→47.268 Å
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Refine LS restraints |
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LS refinement shell |
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