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- PDB-8skp: X-ray structure of the NDM-4 beta-lactamase from Klebsiella pneum... -

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Basic information

Entry
Database: PDB / ID: 8skp
TitleX-ray structure of the NDM-4 beta-lactamase from Klebsiella pneumonia in complex with 1-hydroxypyridine-2(1H)-thione-6-carboxylic acid
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE/INHIBITOR / beta-lactamase / hydrolase / metallo-enzyme / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-WAF / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsThoden, J.B. / Holden, H.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM134643 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Characterization of a novel inhibitor for the New Delhi metallo-beta-lactamase-4: Implications for drug design and combating bacterial drug resistance.
Authors: Thoden, J.B. / Benin, B.M. / Priebe, A. / Shin, W.S. / Muthyala, R. / Sham, Y.Y. / Holden, H.M.
History
DepositionApr 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,5925
Polymers24,2281
Non-polymers3644
Water4,179232
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)40.138, 59.185, 42.266
Angle α, β, γ (deg.)90.00, 98.50, 90.00
Int Tables number4
Space group name H-MP1211

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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: 24228.219 Da / Num. of mol.: 1 / Mutation: M154L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: C7C422, beta-lactamase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-WAF / 1-hydroxy-6-sulfanylidene-1,6-dihydropyridine-2-carboxylic acid


Mass: 171.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.05 Å3/Da / Density % sol: 39.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Protein incubated with 10 mM 1-hydroxypyridine-2(1H)-thione-6-carboxylic acid. Precipitant: 18 - 26% (w/v) poly(ethylene glycol) 3350, 2% (v/v) dimethyl sulfoxide, and 100 mM MES (pH 6.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Jun 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 44587 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rsym value: 0.049 / Net I/σ(I): 16.5
Reflection shellResolution: 1.3→1.4 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 7394 / Rsym value: 0.286 / % possible all: 77.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→32.97 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.302 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22376 2170 4.9 %RANDOM
Rwork0.20243 ---
obs0.20349 42417 92.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.284 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.3→32.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1706 0 17 232 1955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121838
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161637
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.6472503
X-RAY DIFFRACTIONr_angle_other_deg0.4691.5723803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3165242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.04359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65610266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0690.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022165
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02367
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5341.461959
X-RAY DIFFRACTIONr_mcbond_other1.5281.461959
X-RAY DIFFRACTIONr_mcangle_it2.2282.1851201
X-RAY DIFFRACTIONr_mcangle_other2.2292.191202
X-RAY DIFFRACTIONr_scbond_it1.9261.668879
X-RAY DIFFRACTIONr_scbond_other1.9251.671880
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7412.4071302
X-RAY DIFFRACTIONr_long_range_B_refined5.18728.772110
X-RAY DIFFRACTIONr_long_range_B_other5.18628.7852111
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 128 -
Rwork0.296 2518 -
obs--75.09 %

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