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- PDB-6hf5: Crystal Structure of the Acquired VIM-2 Metallo-beta-Lactamase in... -

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Basic information

Entry
Database: PDB / ID: 6hf5
TitleCrystal Structure of the Acquired VIM-2 Metallo-beta-Lactamase in Complex with ANT-431 Inhibitor
ComponentsBeta-lactamase class B VIM-2
KeywordsHYDROLASE / metallo-beta-lactamase fold / zinc-dependent hydrolase / PFam00753 / alpha-beta-beta-alpha sandwich
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
ACETATE ION / Chem-G1N / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDocquier, J.D. / Pozzi, C. / De Luca, F. / Benvenuti, M. / Mangani, S.
CitationJournal: Acs Infect Dis. / Year: 2019
Title: SAR Studies Leading to the Identification of a Novel Series of Metallo-beta-lactamase Inhibitors for the Treatment of Carbapenem-Resistant Enterobacteriaceae Infections That Display Efficacy ...Title: SAR Studies Leading to the Identification of a Novel Series of Metallo-beta-lactamase Inhibitors for the Treatment of Carbapenem-Resistant Enterobacteriaceae Infections That Display Efficacy in an Animal Infection Model.
Authors: Leiris, S. / Coelho, A. / Castandet, J. / Bayet, M. / Lozano, C. / Bougnon, J. / Bousquet, J. / Everett, M. / Lemonnier, M. / Sprynski, N. / Zalacain, M. / Pallin, T.D. / Cramp, M.C. / ...Authors: Leiris, S. / Coelho, A. / Castandet, J. / Bayet, M. / Lozano, C. / Bougnon, J. / Bousquet, J. / Everett, M. / Lemonnier, M. / Sprynski, N. / Zalacain, M. / Pallin, T.D. / Cramp, M.C. / Jennings, N. / Raphy, G. / Jones, M.W. / Pattipati, R. / Shankar, B. / Sivasubrahmanyam, R. / Soodhagani, A.K. / Juventhala, R.R. / Pottabathini, N. / Pothukanuri, S. / Benvenuti, M. / Pozzi, C. / Mangani, S. / De Luca, F. / Cerboni, G. / Docquier, J.D. / Davies, D.T.
History
DepositionAug 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2797
Polymers24,6791
Non-polymers6006
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-106 kcal/mol
Surface area9450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.292, 77.688, 79.327
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Beta-lactamase class B VIM-2 / BlaVIM-2 / Metallo-beta lactamase protein / Metallo-beta-lactamase / Metallo-beta-lactamase VIM-2 / ...BlaVIM-2 / Metallo-beta lactamase protein / Metallo-beta-lactamase / Metallo-beta-lactamase VIM-2 / VIM-2 class B beta-lactamase / VIM-2 class B metallo b-lactamase / VIM-2 metallo-beta-lactamase / VIM-2 type metallo-beta-lactamase


Mass: 24679.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, VIM-2, vim-2, DI492_33875
Plasmid: pET-9a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K2N0
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-G1N / 5-(pyridin-3-ylsulfonylamino)-1,3-thiazole-4-carboxylic acid


Mass: 285.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7N3O4S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.1 Å3/Da / Density % sol: 41.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M cacodylate, 0.2 M Na-acetate, 5 mM DTT, 26% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 30, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.8→51.32 Å / Num. obs: 19621 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 2800 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MXR

5mxr


Resolution: 1.8→51.32 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1052 5.4 %Random selection
Rwork0.184 ---
obs0.187 18569 99.99 %-
Displacement parametersBiso mean: 33.083 Å2
Refinement stepCycle: LAST / Resolution: 1.8→51.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1730 0 29 97 1856

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