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- PDB-9dew: Crystal structure of NDM-1 complexed with compound 2 -

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Basic information

Entry
Database: PDB / ID: 9dew
TitleCrystal structure of NDM-1 complexed with compound 2
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE / Inhibitor / Beta-lactamase / complex / NDM
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 / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsJacobs, L.M.C. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI103158-01A1 United States
CitationJournal: To Be Published
Title: Hit to Lead Optimization of Heteroaryl Phosphonates Reversible, Broad-Spectrum Inhibitors of Serine and Metallo Carbapenemases.
Authors: Jacobs, L.M.C. / Renslo, A.
History
DepositionAug 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3205
Polymers24,6031
Non-polymers7174
Water4,540252
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)40.980, 59.698, 42.400
Angle α, β, γ (deg.)90.00, 93.38, 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: 24602.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: C7C422, beta-lactamase
#2: Chemical ChemComp-A1A4D / [(7-cyclopropyl-1-methyl-2-oxo-1,2-dihydroquinolin-4-yl)methyl]phosphonic acid


Mass: 293.255 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H16NO4P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.1 Å3/Da / Density % sol: 41.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 50 mM Potassium phosphate monobasic, 10 mM Calcium chloride, 25% (w/v) PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 22908 / % possible obs: 94.6 % / Redundancy: 3 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 13.96
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2.24 / Num. unique obs: 1150

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→42.33 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.981 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18828 1071 4.7 %RANDOM
Rwork0.15417 ---
obs0.15592 21585 92.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.717 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20.11 Å2
2---0.01 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: 1 / Resolution: 1.65→42.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1702 0 42 252 1996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131830
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151646
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.6662508
X-RAY DIFFRACTIONr_angle_other_deg1.4631.5813783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1695238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.64523.33387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13415265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.941158
X-RAY DIFFRACTIONr_chiral_restr0.0820.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022159
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02413
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_it1.171.354937
X-RAY DIFFRACTIONr_mcbond_other1.1431.35936
X-RAY DIFFRACTIONr_mcangle_it1.7332.0241177
X-RAY DIFFRACTIONr_mcangle_other1.7412.0281178
X-RAY DIFFRACTIONr_scbond_it1.9251.606893
X-RAY DIFFRACTIONr_scbond_other1.9271.56849
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9012.2511262
X-RAY DIFFRACTIONr_long_range_B_refined4.48218.0082199
X-RAY DIFFRACTIONr_long_range_B_other4.32717.1142003
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.653→1.696 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 46 -
Rwork0.217 1241 -
obs--70.79 %

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