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- PDB-2xtx: Structure of QnrB1 (M102R-Trypsin Treated), a plasmid-mediated fl... -

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Basic information

Entry
Database: PDB / ID: 2xtx
TitleStructure of QnrB1 (M102R-Trypsin Treated), 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 / SYNCHROTRON / SAD / Resolution: 2.2 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 1.2May 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: QNRB1
B: QNRB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4964
Polymers48,3042
Non-polymers1922
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-35.1 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.065, 101.065, 275.609
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-2007-

HOH

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Components

#1: Protein QNRB1


Mass: 24152.076 Da / Num. of mol.: 2
Fragment: TOPISOMERASE POISON RESISTANCE FACTOR, RESIDUES 13-226
Mutation: YES
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
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, MET 114 TO ARG ENGINEERED RESIDUE IN CHAIN B, MET 114 TO ARG
Sequence detailsN-TERMINAL CLEAVABLE TAG LEAVES GSH AT N-TERMINUS. M102R MUTANT. PROTEIN CLONED FROM SECOND ...N-TERMINAL CLEAVABLE TAG LEAVES GSH AT N-TERMINUS. M102R MUTANT. PROTEIN CLONED FROM SECOND METHIONINE COMPARED WITH UNIPROT 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: 3.64 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growTemperature: 293 K / pH: 4.5
Details: 100 MM CITRATE/PHOSPHATE PH 4.5, 1 M AMMONIUM SULFATE AT 20 DEGREES C

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9806
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9806 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 35308 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 35.95 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 27
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 6 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.2→40.748 Å / SU ML: 0.28 / σ(F): 0 / Phase error: 22.33 / Stereochemistry target values: ML
Details: PROTEIN WAS TREATED WITH TRYPSIN PRIOR TO CRYSTALLIZATION. CLIPPING MOST LIKELY AT ARG108.
RfactorNum. reflection% reflection
Rfree0.2222 1768 5 %
Rwork0.1931 --
obs0.1946 35308 95.99 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.017 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso mean: 40.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.394 Å20 Å20 Å2
2--4.394 Å20 Å2
3----8.7879 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3269 0 10 190 3469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073374
X-RAY DIFFRACTIONf_angle_d0.9784541
X-RAY DIFFRACTIONf_dihedral_angle_d13.1351201
X-RAY DIFFRACTIONf_chiral_restr0.069482
X-RAY DIFFRACTIONf_plane_restr0.003598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1996-2.27830.31991710.24293097X-RAY DIFFRACTION91
2.2783-2.36950.27971710.23113165X-RAY DIFFRACTION92
2.3695-2.47730.28691640.21493246X-RAY DIFFRACTION94
2.4773-2.60790.23431580.20713291X-RAY DIFFRACTION95
2.6079-2.77120.25411850.20583339X-RAY DIFFRACTION97
2.7712-2.98510.23531880.20353379X-RAY DIFFRACTION98
2.9851-3.28540.2341640.20553451X-RAY DIFFRACTION99
3.2854-3.76050.20541860.18343476X-RAY DIFFRACTION99
3.7605-4.73670.17431990.15093442X-RAY DIFFRACTION98
4.7367-40.75550.22771820.20783654X-RAY DIFFRACTION97

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