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- PDB-8r5t: Crystal structure of NDM-1 in complex with benzobisheterocycle co... -

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Basic information

Entry
Database: PDB / ID: 8r5t
TitleCrystal structure of NDM-1 in complex with benzobisheterocycle compound 14.
ComponentsMetallo-beta-lactamase type 2
KeywordsANTIMICROBIAL PROTEIN / metallo-beta-lactamase / inhibitor
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc 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
: / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.58 Å
AuthorsHinchliffe, P. / Spencer, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI100560 United States
CitationJournal: J.Med.Chem. / Year: 2024
Title: Rational Design of Benzobisheterocycle Metallo-beta-Lactamase Inhibitors: A Tricyclic Scaffold Enhances Potency against Target Enzymes.
Authors: Villamil, V. / Rossi, M.A. / Mojica, M.F. / Hinchliffe, P. / Martinez, V. / Castillo, V. / Saiz, C. / Banchio, C. / Macias, M.A. / Spencer, J. / Bonomo, R.A. / Vila, A. / Moreno, D.M. / Mahler, G.
History
DepositionNov 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metallo-beta-lactamase type 2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2309
Polymers51,5522
Non-polymers6787
Water6,179343
1
A: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3236
Polymers25,7761
Non-polymers5475
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9073
Polymers25,7761
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.100, 73.768, 77.647
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Metallo-beta-lactamase type 2 / B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta- ...B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta-lactamase type II / New Delhi metallo-beta-lactamase-1 / NDM-1


Mass: 25775.951 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C7C422, beta-lactamase
#2: Chemical ChemComp-Y4E / [(1~{R},3~{a}~{R})-1,3,3~{a},4-tetrahydro-[1,3]thiazolo[3,4-a]benzimidazol-1-yl]methanethiol


Mass: 224.346 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 1.95 Å3/Da / Density % sol: 36.83 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.1M bis-tris pH 5.8, 32% PEG 3350, 0.15M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.87 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.58→35.05 Å / Num. obs: 55898 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rpim(I) all: 0.032 / Net I/σ(I): 13.4
Reflection shellResolution: 1.58→1.61 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2738 / CC1/2: 0.668 / Rpim(I) all: 0.586

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
Aimlessdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.58→34.356 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2127 2751 4.93 %
Rwork0.1688 53064 -
obs0.1711 55815 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.42 Å2 / Biso mean: 28.6065 Å2 / Biso min: 12.51 Å2
Refinement stepCycle: final / Resolution: 1.58→34.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3368 0 40 343 3751
Biso mean--32.45 36.85 -
Num. residues----451
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.5801-1.60730.31471230.23332636
1.6073-1.63650.29591300.21612636
1.6365-1.6680.26331210.19162619
1.668-1.7020.23711520.18162593
1.702-1.73910.28411250.17952622
1.7391-1.77950.28781390.17042625
1.7795-1.8240.22161090.16382641
1.824-1.87330.22671210.15332649
1.8733-1.92840.22851360.14552620
1.9284-1.99070.18621290.14012666
1.9907-2.06180.18641260.14312642
2.0618-2.14440.19311110.13442651
2.1444-2.24190.18491330.14212656
2.2419-2.36010.18791550.14622634
2.3601-2.50790.21321580.15762649
2.5079-2.70150.19641610.15972630
2.7015-2.97320.21441730.17422658
2.9732-3.40310.19951590.16642662
3.4031-4.28630.20081160.1662759
4.2863-34.3560.22291740.20532816

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