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- PDB-2xty: Structure of QnrB1 (R167E-Trypsin Treated), a plasmid-mediated fl... -

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Basic information

Entry
Database: PDB / ID: 2xty
TitleStructure of QnrB1 (R167E-Trypsin Treated), a plasmid-mediated fluoroquinolone resistance protein
ComponentsQNRB1
KeywordsCELL CYCLE / PENTAPEPTIDE REPEAT / PRP / ANTIBIOTIC RESISTANCE / RIGHT HANDED QUADRILATERAL BETA-HELIX
Function / homologyPentapeptide repeat region / : / Pentapeptide repeats (8 copies) / Pentapeptide repeat / E3 ubiquitin-protein ligase SopA / Pectate Lyase C-like / 3 Solenoid / Mainly Beta / QnrB1
Function and homology information
Biological speciesKLEBSIELLA PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 13, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 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
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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


Theoretical massNumber of molelcules
Total (without water)48,1962
Polymers48,1962
Non-polymers00
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-12.4 kcal/mol
Surface area17870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.330, 55.330, 282.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein QNRB1


Mass: 24097.998 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 179 TO GLU ENGINEERED RESIDUE IN CHAIN B, ARG 179 TO GLU
Sequence detailsPROTEIN WAS CLONED FROM SECOND METHIONINE POSITION IN UNIPROT. THERE IS A MUTATION AT RESIDUE ...PROTEIN WAS CLONED FROM SECOND METHIONINE POSITION IN UNIPROT. THERE IS A MUTATION AT RESIDUE POSITION 167(UNIPROT 179), R167E. PROTEIN IS CLEAVED WITH TRYPSIN PRIOR TO CRYSTALLIZATION. CLEAVAGE OCCURS IN THE 102-113 LOOP.

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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: 2.24 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growTemperature: 293 K / pH: 7.5
Details: 100 MM BISTRISPROPANE/CITRATE PH 7.5, 15% PEG 3350 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: 1.8→40 Å / Num. obs: 40346 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 15.69 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.8 / % possible all: 75.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XTX

2xtx


Resolution: 1.8→51.517 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 20.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2209 2003 5.1 %
Rwork0.1798 --
obs0.1819 39399 93.41 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.994 Å2 / ksol: 0.394 e/Å3
Displacement parametersBiso mean: 17.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.4141 Å20 Å20 Å2
2---1.4141 Å20 Å2
3---2.8282 Å2
Refinement stepCycle: LAST / Resolution: 1.8→51.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3211 0 0 323 3534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013275
X-RAY DIFFRACTIONf_angle_d1.184401
X-RAY DIFFRACTIONf_dihedral_angle_d13.6161160
X-RAY DIFFRACTIONf_chiral_restr0.083469
X-RAY DIFFRACTIONf_plane_restr0.005581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.86440.29551420.23782492X-RAY DIFFRACTION64
1.8644-1.9390.24561800.20443107X-RAY DIFFRACTION80
1.939-2.02730.22811960.17163626X-RAY DIFFRACTION92
2.0273-2.13420.20732020.16513875X-RAY DIFFRACTION98
2.1342-2.26790.22132010.16683892X-RAY DIFFRACTION99
2.2679-2.4430.19712100.17843968X-RAY DIFFRACTION100
2.443-2.68880.25531960.19184011X-RAY DIFFRACTION100
2.6888-3.07780.2272210.1944015X-RAY DIFFRACTION100
3.0778-3.87760.21682340.17434056X-RAY DIFFRACTION100
3.8776-51.53860.2012210.17074354X-RAY DIFFRACTION100

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