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- PDB-6sp7: Crystal Structure of the VIM-2 Acquired Metallo-beta-Lactamase in... -

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Basic information

Entry
Database: PDB / ID: 6sp7
TitleCrystal Structure of the VIM-2 Acquired Metallo-beta-Lactamase in Complex with Taniborbactam (VNRX-5133)
ComponentsMetallo-beta-lactamase VIM-2
KeywordsHYDROLASE / Metallo-carbapenemase / antibiotic resistance / metallo-beta-lactamase superfamily / zinc-hydrolase / taniborbactam / beta-lactamase inhibitor
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-K9B / Metallo-beta-lactamase type 2 / Metallo-beta-lactamase VIM-2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsDocquier, J.D. / Pozzi, C. / De Luca, F. / Benvenuti, M. / Mangani, S.
Citation
Journal: J.Med.Chem. / Year: 2020
Title: Discovery of Taniborbactam (VNRX-5133): A Broad-Spectrum Serine- and Metallo-beta-lactamase Inhibitor for Carbapenem-Resistant Bacterial Infections.
Authors: Liu, B. / Trout, R.E.L. / Chu, G.H. / McGarry, D. / Jackson, R.W. / Hamrick, J.C. / Daigle, D.M. / Cusick, S.M. / Pozzi, C. / De Luca, F. / Benvenuti, M. / Mangani, S. / Docquier, J.D. / ...Authors: Liu, B. / Trout, R.E.L. / Chu, G.H. / McGarry, D. / Jackson, R.W. / Hamrick, J.C. / Daigle, D.M. / Cusick, S.M. / Pozzi, C. / De Luca, F. / Benvenuti, M. / Mangani, S. / Docquier, J.D. / Weiss, W.J. / Pevear, D.C. / Xerri, L. / Burns, C.J.
#1: Journal: Antimicrob. Agents Chemother. / Year: 2019
Title: VNRX-5133 (Taniborbactam), a broad-spectrum inhibitor of serine- and metallo-beta-lactamases, restores activity of cefepime in Enterobacterales and Pseudomonas aeruginosa.
Authors: Hamrick, J.C. / Docquier, J.D. / Uehara, T. / Myers, C.L. / Six, D.A. / Chatwin, C.L. / John, K.J. / Vernacchio, S.F. / Cusick, S.M. / Trout, R.E.L. / Pozzi, C. / De Luca, F. / Benvenuti, M. ...Authors: Hamrick, J.C. / Docquier, J.D. / Uehara, T. / Myers, C.L. / Six, D.A. / Chatwin, C.L. / John, K.J. / Vernacchio, S.F. / Cusick, S.M. / Trout, R.E.L. / Pozzi, C. / De Luca, F. / Benvenuti, M. / Mangani, S. / Liu, B. / Jackson, R.W. / Moeck, G. / Xerri, L. / Burns, C.J. / Pevear, D.C. / Daigle, D.M.
History
DepositionAug 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 24, 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_asym_id / _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_asym_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: Metallo-beta-lactamase VIM-2
E: Metallo-beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,48614
Polymers49,0442
Non-polymers1,44112
Water3,603200
1
A: Metallo-beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2437
Polymers24,5221
Non-polymers7216
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Metallo-beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2437
Polymers24,5221
Non-polymers7216
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.910, 79.040, 67.490
Angle α, β, γ (deg.)90.000, 130.500, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Metallo-beta-lactamase VIM-2


Mass: 24522.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: pET-9a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: S5M6K4, UniProt: Q9K2N0*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-K9B / (4~{R})-4-[2-[4-(2-azanylethylamino)cyclohexyl]ethanoylamino]-3,3-bis(oxidanyl)-2-oxa-3-boranuidabicyclo[4.4.0]deca-1(10),6,8-triene-10-carboxylic acid


Mass: 406.261 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H29BN3O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 42.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M cacodilate (pH 6.5), 5 mM DTT , 0.2 M Na-acetate, 26% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 18, 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: 1.8→55.609 Å / Num. all: 36880 / Num. obs: 36880 / % possible obs: 96.9 % / Redundancy: 3 % / Rpim(I) all: 0.064 / Rrim(I) all: 0.114 / Rsym value: 0.08 / Net I/av σ(I): 6.8 / Net I/σ(I): 7.4 / Num. measured all: 110379
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.8-1.930.3831.91573452920.3080.5460.3832.296
1.9-2.0130.2582.81486550340.2080.3690.2583.296
2.01-2.1530.18141446447630.140.2510.1814.796.6
2.15-2.3230.1355.41361144730.1070.1910.1355.896.9
2.32-2.5530.0967.41204640720.0790.1390.0967.397.1
2.55-2.8530.0798.71118637290.0620.110.0799.197.4
2.85-3.2930.0610.6984533010.0470.0840.0611.697.6
3.29-4.0230.04812.4856128210.0390.070.04814.798.3
4.02-5.6930.04911.6646121700.0370.0670.04915.697.8
5.69-28.9252.90.0449.5360612250.0380.0680.04414.998

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLM7.1.1data reduction
SCALA3.3.21data scaling
MOLREP11.2.08phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KO3

1ko3


Resolution: 1.8→28.92 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.815 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 1894 5.1 %RANDOM
Rwork0.189 ---
obs0.1919 34979 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.14 Å2 / Biso mean: 22.42 Å2 / Biso min: 4.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2--0.01 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.8→28.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 80 200 3746
Biso mean--23.07 28.68 -
Num. residues----460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193635
X-RAY DIFFRACTIONr_bond_other_d0.0030.023384
X-RAY DIFFRACTIONr_angle_refined_deg2.0671.9744978
X-RAY DIFFRACTIONr_angle_other_deg1.11637782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8135462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.20124.026154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.89415518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6841520
X-RAY DIFFRACTIONr_chiral_restr0.1750.2569
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214172
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02806
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 114 -
Rwork0.28 2574 -
all-2688 -
obs--95.97 %

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