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- PDB-9db7: Crystal structure of NDM-1 complexed with compound 22 -

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Basic information

Entry
Database: PDB / ID: 9db7
TitleCrystal structure of NDM-1 complexed with compound 22
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: 1.78 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. / Chen, Y. / Renslo, A.
History
DepositionAug 23, 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
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,21611
Polymers49,2052
Non-polymers2,0119
Water4,810267
1
A: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5625
Polymers24,6031
Non-polymers9594
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6546
Polymers24,6031
Non-polymers1,0515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.772, 58.685, 62.242
Angle α, β, γ (deg.)90.00, 90.89, 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.: 2
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-A1A14 / {[7-bromo-1-(cyclopentylmethyl)-3-methyl-2-oxo-1,2-dihydroquinolin-4-yl]methyl}phosphonic acid


Mass: 414.231 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21BrNO4P / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 M Bis Tris pH 7.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 38500 / % possible obs: 98.1 % / Redundancy: 4 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 21.63
Reflection shellResolution: 1.78→1.81 Å / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 2.57 / Num. unique obs: 1853

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→42.73 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.715 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21227 1995 5.2 %RANDOM
Rwork0.16118 ---
obs0.16373 36491 97.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.912 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20.53 Å2
2---1.8 Å20 Å2
3---1.94 Å2
Refinement stepCycle: 1 / Resolution: 1.78→42.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3404 0 106 267 3777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133602
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153238
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.6724921
X-RAY DIFFRACTIONr_angle_other_deg1.441.587431
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0085458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.33123.054167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06115513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9651516
X-RAY DIFFRACTIONr_chiral_restr0.0790.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024174
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02802
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_it1.8472.4361835
X-RAY DIFFRACTIONr_mcbond_other1.8392.4341834
X-RAY DIFFRACTIONr_mcangle_it2.5233.6442292
X-RAY DIFFRACTIONr_mcangle_other2.5273.6462293
X-RAY DIFFRACTIONr_scbond_it2.8132.7421767
X-RAY DIFFRACTIONr_scbond_other2.8022.731716
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0823.9722552
X-RAY DIFFRACTIONr_long_range_B_refined5.03329.6974179
X-RAY DIFFRACTIONr_long_range_B_other4.97729.5093978
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.781→1.827 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 116 -
Rwork0.216 2586 -
obs--93.88 %

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