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- PDB-6tgd: Crystal structure of NDM-1 in complex with triazole-based inhibit... -

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Basic information

Entry
Database: PDB / ID: 6tgd
TitleCrystal structure of NDM-1 in complex with triazole-based inhibitor OP31
ComponentsMetallo-beta-lactamase NDM-1
KeywordsHYDROLASE / New Delhi 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-N8Q / Metallo-beta-lactamase NDM-1
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsMaso, L. / Spirakis, F. / Santucci, M. / Simon, C. / Docquier, J.D. / Cruciani, G. / Costi, M.P. / Tondi, D. / Cendron, L.
Funding support Italy, 1items
OrganizationGrant numberCountry
European Communitys Seventh Framework Programme286998 Italy
CitationJournal: Sci Rep / Year: 2020
Title: Virtual screening identifies broad-spectrum beta-lactamase inhibitors with activity on clinically relevant serine- and metallo-carbapenemases.
Authors: Spyrakis, F. / Santucci, M. / Maso, L. / Cross, S. / Gianquinto, E. / Sannio, F. / Verdirosa, F. / De Luca, F. / Docquier, J.D. / Cendron, L. / Tondi, D. / Venturelli, A. / Cruciani, G. / Costi, M.P.
History
DepositionNov 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)51,89612
Polymers50,9492
Non-polymers94710
Water6,233346
1
A: Metallo-beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9486
Polymers25,4751
Non-polymers4735
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9486
Polymers25,4751
Non-polymers4735
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.678, 73.665, 77.501
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 NDM-1


Mass: 25474.627 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: not visible in the electron density / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaNDM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: M4JT39
#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-N8Q / 4-[[(2~{S})-oxolan-2-yl]methyl]-3-pyridin-3-yl-1~{H}-1,2,4-triazole-5-thione


Mass: 262.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H14N4OS / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 36.99 %
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: SLS / Beamline: X06DA / Wavelength: 1.001 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.001 Å / Relative weight: 1
ReflectionResolution: 1.33→42.42 Å / Num. obs: 89075 / % possible obs: 97.4 % / Redundancy: 1.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Net I/σ(I): 10.3
Reflection shellResolution: 1.33→1.38 Å / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 8196 / CC1/2: 0.714 / % possible all: 93.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IBV

6ibv


Resolution: 1.33→42.42 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.061 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2073 4611 5.2 %RANDOM
Rwork0.1853 ---
obs0.1865 84461 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 66.19 Å2 / Biso mean: 19.037 Å2 / Biso min: 8.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å2-0 Å2-0 Å2
2---0.25 Å20 Å2
3---1.11 Å2
Refinement stepCycle: final / Resolution: 1.33→42.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3418 0 44 346 3808
Biso mean--31.1 26.6 -
Num. residues----460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123653
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.6384992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6415486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.74923.023172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47815551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6521517
X-RAY DIFFRACTIONr_chiral_restr0.110.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022866
X-RAY DIFFRACTIONr_rigid_bond_restr7.61433653
LS refinement shellResolution: 1.332→1.367 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.598 358 -
Rwork0.59 5939 -
all-6297 -
obs--93.73 %

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