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- PDB-8b20: NDM-1 metallo-beta-lactamase in complex with triazole-based inhib... -

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Basic information

Entry
Database: PDB / ID: 8b20
TitleNDM-1 metallo-beta-lactamase in complex with triazole-based inhibitor CP57
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-OQK / Beta-lactamase NDM-1
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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)52,46214
Polymers51,2642
Non-polymers1,19912
Water2,414134
1
A: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2977
Polymers25,6321
Non-polymers6656
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1657
Polymers25,6321
Non-polymers5336
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.068, 70.444, 73.803
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, 146 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.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-OQK / 2-[(~{E})-[3-sulfanyl-5-[4-(trifluoromethyl)phenyl]-1,2,4-triazol-4-yl]iminomethyl]benzoic acid


Mass: 392.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H11F3N4O2S / Feature type: SUBJECT OF INVESTIGATION
#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.: 134 / 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: 37.05 %
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 hexahydrate, 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: 1.78→53.31 Å / Num. obs: 39230 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.178 / Net I/σ(I): 6.8
Reflection shellResolution: 1.78→1.82 Å / Redundancy: 7 % / Rmerge(I) obs: 0.956 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2195 / % possible all: 100

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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: 1.78→53.306 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.117 / Details: Hydrogens have not been used
RfactorNum. reflection% reflectionSelection details
Rfree0.2073 1900 4.851 %RANDOM
Rwork0.184 37269 --
all0.185 ---
obs-39169 99.931 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26 Å2
Baniso -1Baniso -2Baniso -3
1-0.603 Å2-0 Å2-0 Å2
2--1.418 Å2-0 Å2
3----2.021 Å2
Refinement stepCycle: LAST / Resolution: 1.78→53.306 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3434 0 61 134 3629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123576
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.6274867
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7775462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.70823.095168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67315521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.341516
X-RAY DIFFRACTIONr_chiral_restr0.1050.2472
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022758
X-RAY DIFFRACTIONr_nbd_refined0.2260.21609
X-RAY DIFFRACTIONr_nbtor_refined0.3180.22415
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2164
X-RAY DIFFRACTIONr_metal_ion_refined0.1140.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3280.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1970.222
X-RAY DIFFRACTIONr_mcbond_it2.1822.3871851
X-RAY DIFFRACTIONr_mcangle_it3.0653.5622312
X-RAY DIFFRACTIONr_scbond_it3.2782.7421725
X-RAY DIFFRACTIONr_scangle_it4.8623.952555
X-RAY DIFFRACTIONr_lrange_it6.14533.4395279
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.78-1.8260.2461440.23427160.23528610.8660.86999.9650.23
1.826-1.8760.2251450.21426230.21527690.9010.89599.96390.207
1.876-1.930.2721340.20125680.20427020.8950.9111000.196
1.93-1.990.1931320.18325220.18426540.9330.931000.18
1.99-2.0550.2151170.18824390.18925560.930.9331000.184
2.055-2.1270.2011110.18823730.18924840.9380.9391000.186
2.127-2.2070.225960.1822830.18223790.9280.9411000.178
2.207-2.2970.224810.17122010.17322820.9330.9491000.17
2.297-2.3990.209910.17621170.17722080.9410.9471000.177
2.399-2.5160.251960.19720390.221360.9220.94199.95320.2
2.516-2.6520.2861080.20219060.20620140.9220.9341000.209
2.652-2.8120.2141020.20318190.20419270.9350.94499.68860.214
2.812-3.0060.208920.18517090.18618020.9510.95399.94450.198
3.006-3.2460.171920.17915980.17816910.9580.95699.94090.201
3.246-3.5540.1791080.17114630.17215730.9620.9699.87290.194
3.554-3.9710.232500.17613630.17814150.9260.95599.85870.206
3.971-4.5810.144610.16712070.16612680.9670.9591000.198
4.581-5.6010.269530.17410340.17810880.9170.96199.90810.212
5.601-7.8770.216590.1888040.198630.9450.9591000.232
7.877-53.3060.122280.1814850.1785240.9850.96997.90080.477

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