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- PDB-8b1w: NDM-1 metallo-beta-lactamase in complex with triazole-based inhib... -

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Basic information

Entry
Database: PDB / ID: 8b1w
TitleNDM-1 metallo-beta-lactamase in complex with triazole-based inhibitor CP35
ComponentsBeta-lactamase NDM-1
KeywordsHYDROLASE / Beta-lactamase / Antibiotic resistance / Beta-lactamase inhibitor
Function / homology: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / metal ion binding / Chem-OQU / Beta-lactamase NDM-1
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVascon, F. / Lazzarato, L. / Bersani, M. / Gianquinto, E. / Docquier, J.D. / Spyrakis, F. / Tondi, D. / Cendron, L.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of Education Italy
CitationJournal: Pharmaceuticals / Year: 2023
Title: Structure-Based Optimization of 1,2,4-Triazole-3-Thione Derivatives: Improving Inhibition of NDM-/VIM-Type Metallo-beta-Lactamases and Synergistic Activity on Resistant Bacteria.
Authors: Bersani, M. / Failla, M. / Vascon, F. / Gianquinto, E. / Bertarini, L. / Baroni, M. / Cruciani, G. / Verdirosa, F. / Sannio, F. / Docquier, J.D. / Cendron, L. / Spyrakis, F. / Lazzarato, L. / Tondi, D.
History
DepositionSep 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase NDM-1
B: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,81216
Polymers51,2642
Non-polymers1,54914
Water2,756153
1
A: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2567
Polymers25,6321
Non-polymers6246
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5569
Polymers25,6321
Non-polymers9258
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.190, 73.699, 77.280
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 Beta-lactamase NDM-1 / Metallo-beta-lactamase / Metallo-beta-lactamase NDM-1 / New Delhi metallo-beta-lactamase 1 / ...Metallo-beta-lactamase / Metallo-beta-lactamase NDM-1 / New Delhi metallo-beta-lactamase 1 / Subclass B1 metallo-beta-lactamase NDM-1


Mass: 25631.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaNDM-1, blaNDM1, E5D53_33975 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F6IAY7

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Non-polymers , 6 types, 167 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-OQU / 4-[(~{E})-(3-bromophenyl)methylideneamino]-5-(trifluoromethyl)-1,2,4-triazole-3-thiol


Mass: 351.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H6BrF3N4S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 1.95 Å3/Da / Density % sol: 36.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES, 0.1 M MOPS, pH 7.5, 0.03 M MgCl2 exahydrate, 0.03 M CaCl2 dihydrate, 12.5% v/v MPD, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.873 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.7→36.88 Å / Num. obs: 44671 / % possible obs: 99.7 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.194 / Net I/σ(I): 8.6
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.531 / Num. unique obs: 2328 / % possible all: 99.5

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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: 1.7→36.88 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2224 2185 5 %RANDOM
Rwork0.1915 ---
obs0.193 44139 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.83 Å2 / Biso mean: 22 Å2 / Biso min: 12.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0 Å2
2--0.02 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 1.7→36.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3434 0 73 153 3660
Biso mean--33.49 25.99 -
Num. residues----462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123587
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.6284883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8425462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.20923.095168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75415521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3371516
X-RAY DIFFRACTIONr_chiral_restr0.1060.2473
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022762
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 148 -
Rwork0.32 3010 -
all-3158 -
obs--96.93 %

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