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- PDB-6efj: Crystal structure of NDM-1 with compound 9 -

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Basic information

Entry
Database: PDB / ID: 6efj
TitleCrystal structure of NDM-1 with compound 9
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Carbapenemase / tetrazole / inhibitor / complex / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
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 / 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-O5E / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsAkhtar, A. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI103158 United States
CitationJournal: Acs Infect Dis. / Year: 2019
Title: Active-Site Druggability of Carbapenemases and Broad-Spectrum Inhibitor Discovery.
Authors: Torelli, N.J. / Akhtar, A. / DeFrees, K. / Jaishankar, P. / Pemberton, O.A. / Zhang, X. / Johnson, C. / Renslo, A.R. / Chen, Y.
History
DepositionAug 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: 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 type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0284
Polymers24,6031
Non-polymers4253
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.980, 58.770, 41.980
Angle α, β, γ (deg.)90.000, 97.480, 90.000
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 / Fragment: residues 42-270
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-O5E / (2R)-2-phenyl-2-(phenylamino)-N-(1H-tetrazol-5-yl)acetamide


Mass: 294.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14N6O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.05 M Potassium Phosphate, 0.01 M Calcium Chloride, 25%(w/v) PEG-8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.65→33.97 Å / Num. obs: 22276 / % possible obs: 91.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 12.8 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.063 / Rrim(I) all: 0.119 / Rsym value: 0.101 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
1.65-1.743.40.51629220.6740.0320.0590.04982.6
5.22-33.973.30.0497450.9950.0290.0560.04793.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.65 Å33.97 Å
Translation1.65 Å33.97 Å

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Processing

Software
NameVersionClassification
iMOSFLM7.2.1data reduction
SCALA3.3.22data scaling
PHASER2.6.0phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TZF

4tzf


Resolution: 1.65→33.967 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.73
RfactorNum. reflection% reflection
Rfree0.2216 1992 8.95 %
Rwork0.1757 --
obs0.1798 22246 90.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 44.84 Å2 / Biso mean: 16.8523 Å2 / Biso min: 4.36 Å2
Refinement stepCycle: final / Resolution: 1.65→33.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 24 243 1968
Biso mean--23.5 24.87 -
Num. residues----229
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.69130.29161220.21661300142281
1.6913-1.7370.23991270.2141295142283
1.737-1.78810.2621250.20921348147385
1.7881-1.84580.27131400.21581401154188
1.8458-1.91180.27111400.21191403154389
1.9118-1.98830.27381440.1911442158692
1.9883-2.07880.20561520.17931482163493
2.0788-2.18840.24011480.17881481162994
2.1884-2.32550.23381520.18531511166394
2.3255-2.5050.2491430.18731487163094
2.505-2.7570.2231530.18141506165995
2.757-3.15570.23461520.17571508166095
3.1557-3.97480.18931440.14771546169096
3.9748-33.9740.16561500.14541544169494

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