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- PDB-6f2n: Crystal structure of BCII Metallo-beta-lactamase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6f2n
TitleCrystal structure of BCII Metallo-beta-lactamase in complex with KDU197
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE / ANTIMICROBIAL RESISTANCE / METALLO BETA LACTAMASE / INHIBITOR
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
: / Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Chem-CF8 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.149 Å
AuthorsMcDonough, M.A. / El-Hussein, A. / Schofield, C.J. / Zhang, D. / Brem, J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
Wellcome Trust United Kingdom
CitationJournal: Bioorg. Med. Chem. / Year: 2018
Title: Structure activity relationship studies on rhodanines and derived enethiol inhibitors of metallo-beta-lactamases.
Authors: Zhang, D. / Markoulides, M.S. / Stepanovs, D. / Rydzik, A.M. / El-Hussein, A. / Bon, C. / Kamps, J.J.A.G. / Umland, K.D. / Collins, P.M. / Cahill, S.T. / Wang, D.Y. / von Delft, F. / Brem, J. ...Authors: Zhang, D. / Markoulides, M.S. / Stepanovs, D. / Rydzik, A.M. / El-Hussein, A. / Bon, C. / Kamps, J.J.A.G. / Umland, K.D. / Collins, P.M. / Cahill, S.T. / Wang, D.Y. / von Delft, F. / Brem, J. / McDonough, M.A. / Schofield, C.J.
History
DepositionNov 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5435
Polymers24,9961
Non-polymers5474
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-19 kcal/mol
Surface area9810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.169, 61.668, 69.675
Angle α, β, γ (deg.)90.000, 93.130, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-415-

HOH

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Components

#1: Protein Metallo-beta-lactamase type 2 / B2 metallo-beta-lactamase / Beta-lactamase II / Cephalosporinase / Metallo-beta-lactamase type II / ...B2 metallo-beta-lactamase / Beta-lactamase II / Cephalosporinase / Metallo-beta-lactamase type II / Metallothioprotein beta-lactamase II / Penicillinase / Zinc-requiring beta-lactamase II


Mass: 24995.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: blm / Plasmid: PET9A
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P04190, beta-lactamase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CF8 / (~{Z})-3-[2-(naphthalen-2-ylmethyl)phenyl]-2-sulfanyl-prop-2-enoic acid


Mass: 320.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H16O2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M A.S., 0.1M BIS-TRIS, 25% PEG 3350, 10mM inhibitor

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 8, 2015 / Details: mirrors
RadiationMonochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.149→28.189 Å / Num. obs: 77781 / % possible obs: 97.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 11.65 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.069 / Net I/σ(I): 14.2
Reflection shellResolution: 1.15→1.18 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5393 / CC1/2: 0.753 / Rrim(I) all: 0.934 / % possible all: 91.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TYT

4tyt


Resolution: 1.149→28.189 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.3
RfactorNum. reflection% reflection
Rfree0.1511 2001 2.57 %
Rwork0.1342 --
obs0.1347 77736 97.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 52.35 Å2 / Biso mean: 19.859 Å2 / Biso min: 7.41 Å2
Refinement stepCycle: final / Resolution: 1.149→28.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1671 0 30 340 2041
Biso mean--28.68 31.66 -
Num. residues----219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191821
X-RAY DIFFRACTIONf_angle_d1.5522485
X-RAY DIFFRACTIONf_chiral_restr0.119291
X-RAY DIFFRACTIONf_plane_restr0.012339
X-RAY DIFFRACTIONf_dihedral_angle_d13.251679
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.149-1.17780.32131350.31375057519291
1.1778-1.20960.30241380.26865247538594
1.2096-1.24520.25311440.2445213535795
1.2452-1.28540.25641360.23365309544596
1.2854-1.33130.23311400.20095334547496
1.3313-1.38460.17461500.1655364551497
1.3846-1.44770.16981390.1185454559398
1.4477-1.5240.12911480.1045463561199
1.524-1.61950.12931460.09295490563699
1.6195-1.74450.13451340.09755493562799
1.7445-1.920.12091530.10345525567899
1.92-2.19770.13841430.109755525695100
2.1977-2.76850.12661480.12955785726100
2.7685-28.19790.14411470.137956565803100

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