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- PDB-2xtw: Structure of QnrB1 (Full length), a plasmid-mediated fluoroquinol... -

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Basic information

Entry
Database: PDB / ID: 2xtw
TitleStructure of QnrB1 (Full length), a plasmid-mediated fluoroquinolone resistance protein
ComponentsQNRB1
KeywordsCELL CYCLE / PENTAPEPTIDE REPEAT / PRP / ANTIBIOTIC RESISTANCE / RIGHT HANDED QUADRILATERAL BETA-HELIX
Function / homologyE3 ubiquitin-protein ligase SopA / Pentapeptide repeats (9 copies) / Pentapeptide repeat / Pectate Lyase C-like / 3 Solenoid / Mainly Beta / QnrB1
Function and homology information
Biological speciesKLEBSIELLA PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.803 Å
AuthorsVetting, M.W. / Hegde, S.S. / Park, C.H. / Jacoby, G.A. / Hooper, D.C. / Blanchard, J.S.
CitationJournal: 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
DepositionOct 12, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2011Group: Database references / Version format compliance
Revision 1.2Apr 3, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: QNRB1
B: QNRB1
C: QNRB1
D: QNRB1


Theoretical massNumber of molelcules
Total (without water)96,5044
Polymers96,5044
Non-polymers00
Water00
1
A: QNRB1
D: QNRB1


Theoretical massNumber of molelcules
Total (without water)48,2522
Polymers48,2522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-9.6 kcal/mol
Surface area19130 Å2
MethodPISA
2
B: QNRB1
C: QNRB1


Theoretical massNumber of molelcules
Total (without water)48,2522
Polymers48,2522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-11.5 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.050, 119.532, 231.725
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
QNRB1


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 detailsCLONED 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

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growTemperature: 277 K / pH: 4.5
Details: 100 MM NA/K PHOSPHATE PH 4.5, 2 M NACL AT 4 DEGREES C

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.8→2.9 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 6.5 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
MOSFLMphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.301 1301 5 %
Rwork0.2247 --
obs0.2286 26120 96.49 %
Solvent computationShrinkage 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 parametersBiso mean: 38.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.9927 Å20 Å20 Å2
2--20.7148 Å20 Å2
3----21.7075 Å2
Refinement stepCycle: LAST / Resolution: 2.803→47.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6610 0 0 0 6610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086732
X-RAY DIFFRACTIONf_angle_d1.1899053
X-RAY DIFFRACTIONf_dihedral_angle_d15.7282393
X-RAY DIFFRACTIONf_chiral_restr0.086964
X-RAY DIFFRACTIONf_plane_restr0.0031187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8031-2.91530.46551270.33912607X-RAY DIFFRACTION92
2.9153-3.04790.40821200.28822589X-RAY DIFFRACTION93
3.0479-3.20860.30941560.24822694X-RAY DIFFRACTION96
3.2086-3.40960.33921440.23622688X-RAY DIFFRACTION96
3.4096-3.67270.31481590.22822702X-RAY DIFFRACTION96
3.6727-4.04210.23411470.19292786X-RAY DIFFRACTION98
4.0421-4.62660.23721280.16382874X-RAY DIFFRACTION99
4.6266-5.82740.27091530.20422849X-RAY DIFFRACTION99
5.8274-47.27520.32351670.25733030X-RAY DIFFRACTION98

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