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- PDB-8a76: Metallo-beta-lactamase NDM-1 in complex with 1,2,4-Triazole-3-thi... -

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Basic information

Entry
Database: PDB / ID: 8a76
TitleMetallo-beta-lactamase NDM-1 in complex with 1,2,4-Triazole-3-thione compound 26
ComponentsMetallo-beta-lactamase NDM-1
KeywordsHYDROLASE / Metallo-beta-lactamase
Function / homology
Function and homology information


antibiotic catabolic process / metal ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-L82 / DI(HYDROXYETHYL)ETHER / Metallo-beta-lactamase NDM-1
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsVascon, F. / Legru, A. / Hernandez, J.F. / Cendron, L.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of Education Italy
CitationJournal: J.Med.Chem. / Year: 2022
Title: Optimization of 1,2,4-Triazole-3-thiones toward Broad-Spectrum Metallo-beta-lactamase Inhibitors Showing Potent Synergistic Activity on VIM- and NDM-1-Producing Clinical Isolates.
Authors: Legru, A. / Verdirosa, F. / Vo-Hoang, Y. / Tassone, G. / Vascon, F. / Thomas, C.A. / Sannio, F. / Corsica, G. / Benvenuti, M. / Feller, G. / Coulon, R. / Marcoccia, F. / Devente, S.R. / ...Authors: Legru, A. / Verdirosa, F. / Vo-Hoang, Y. / Tassone, G. / Vascon, F. / Thomas, C.A. / Sannio, F. / Corsica, G. / Benvenuti, M. / Feller, G. / Coulon, R. / Marcoccia, F. / Devente, S.R. / Bouajila, E. / Piveteau, C. / Leroux, F. / Deprez-Poulain, R. / Deprez, B. / Licznar-Fajardo, P. / Crowder, M.W. / Cendron, L. / Pozzi, C. / Mangani, S. / Docquier, J.D. / Hernandez, J.F. / Gavara, L.
History
DepositionJun 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallo-beta-lactamase NDM-1
B: Metallo-beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,11125
Polymers50,9492
Non-polymers2,16223
Water5,368298
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.332, 73.904, 77.288
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Metallo-beta-lactamase NDM-1


Mass: 25474.627 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaNDM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: M4JT39

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Non-polymers , 7 types, 321 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-L82 / (2~{S})-2-[bis(pyridin-2-ylmethyl)amino]-5-(3-phenyl-5-sulfanylidene-1~{H}-1,2,4-triazol-4-yl)pentanoic acid


Mass: 474.578 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H26N6O2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H18N2O4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.06 Å3/Da / Density % sol: 40.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.3 M MgCl2 exahydrate; 0.3 M CaCl2 dihydrate; 25% w/v PEG 3350; 25% w/v MPD; 20% v/v PEG 1000; 0.1 M MES/IMIDAZOLE pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.5→42.57 Å / Num. obs: 65206 / % possible obs: 100 % / Redundancy: 18.3 % / CC1/2: 1 / Rrim(I) all: 0.078 / Net I/σ(I): 21.5
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 3187 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TGD

6tgd


Resolution: 1.5→42.57 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.259 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1881 3241 5 %RANDOM
Rwork0.1658 ---
obs0.1669 61894 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.28 Å2 / Biso mean: 23.033 Å2 / Biso min: 10.05 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å2-0 Å2-0 Å2
2---1.44 Å2-0 Å2
3---0.26 Å2
Refinement stepCycle: final / Resolution: 1.5→42.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3434 0 124 297 3855
Biso mean--41.53 32.7 -
Num. residues----462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0123755
X-RAY DIFFRACTIONr_angle_refined_deg1.951.6485099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7455489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.41623.064173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63915548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9431517
X-RAY DIFFRACTIONr_chiral_restr0.1160.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022892
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 272 -
Rwork0.267 4471 -
all-4743 -
obs--99.77 %

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