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- PDB-5mxq: Crystal Structure of the Acquired VIM-2 Metallo-beta-Lactamase in... -

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Basic information

Entry
Database: PDB / ID: 5mxq
TitleCrystal Structure of the Acquired VIM-2 Metallo-beta-Lactamase in Complex with ANT-90 Inhibitor
ComponentsBeta-lactamase VIM-2
KeywordsHYDROLASE / metallo-beta-lactamase fold / zinc-dependent hydrolase / PFam00753 / alpha-beta-beta-alpha sandwich / metallo-beta-lactamase inhibitor
Function / homology
Function and homology information


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 / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 3-(phenylsulfonylamino)pyridine-2-carboxylic acid / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDocquier, J.D. / De Luca, F. / Benvenuti, M. / Di Pisa, F. / Pozzi, C. / 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
DepositionJan 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / 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.identifier_ORCID / _citation_author.name
Revision 1.3Jan 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.ptnr2_symmetry / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,3078
Polymers24,6791
Non-polymers6287
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-119 kcal/mol
Surface area9510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.909, 77.900, 79.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase VIM-2 / Class B beta-lactamase / Class B carbapenemase VIM-2 / Metallo beta lactamase VIM-2 / Metallo beta- ...Class B beta-lactamase / Class B carbapenemase VIM-2 / Metallo beta lactamase VIM-2 / Metallo beta-lactamase / Metallo-beta-lactamase / Metallo-beta-lactamase VIM-2 / Metallo-beta-lactamase vim-2 / VIM-2 metallo-beta-lactamase / VIM-2 protein


Mass: 24679.439 Da / Num. of mol.: 1 / Fragment: VIM-2 mature protein
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, blm, VIM-2, vim-2, PAERUG_P32_London_17_VIM_2_10_11_06255
Plasmid: pET-9a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K2N0

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Non-polymers , 5 types, 83 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-U8K / 3-(phenylsulfonylamino)pyridine-2-carboxylic acid


Mass: 278.284 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10N2O4S
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.13 Å3/Da / Density % sol: 42.22 % / Mosaicity: 0.84 °
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 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 4, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→31.38 Å / Num. obs: 14585 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.055 / Rrim(I) all: 0.139 / Net I/σ(I): 9.8 / Num. measured all: 91927 / Scaling rejects: 26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.066.40.7040.8410.3020.767100
8.49-31.385.70.0440.9980.020.04898.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
Aimless0.3.11data scaling
PDB_EXTRACT3.22data extraction
iMOSFLM7.2.1data reduction
MOLREP11.4.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KO3

1ko3


Resolution: 2→31.09 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.712 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.195 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.227 755 5.2 %RANDOM
Rwork0.1764 ---
obs0.179 13828 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.95 Å2 / Biso mean: 26.195 Å2 / Biso min: 12.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2→31.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1740 0 31 76 1847
Biso mean--21.45 26.64 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191836
X-RAY DIFFRACTIONr_bond_other_d0.0030.021687
X-RAY DIFFRACTIONr_angle_refined_deg1.8821.9622516
X-RAY DIFFRACTIONr_angle_other_deg1.083.0023874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0085236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.48123.95181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25915260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3571511
X-RAY DIFFRACTIONr_chiral_restr0.1070.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212139
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02421
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 40 -
Rwork0.246 1015 -
all-1055 -
obs--100 %

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