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- PDB-6mdu: Crystal structure of NDM-1 with compound 7 -

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Basic information

Entry
Database: PDB / ID: 6mdu
TitleCrystal structure of NDM-1 with compound 7
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE/INHIBITOR / Carbapenemase / tetrazole / inhibitor / complex / HYDROLASE / 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-N1G / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.15 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
DepositionSep 5, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,1575
Polymers24,6031
Non-polymers5544
Water5,459303
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)41.680, 58.870, 42.030
Angle α, β, γ (deg.)90.000, 98.170, 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
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-N1G / 1,5-diphenyl-N-(1H-tetrazol-5-yl)-1H-pyrazole-3-carboxamide


Mass: 331.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H13N7O / Feature type: SUBJECT OF INVESTIGATION
#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.: 303 / 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: 2.07 Å3/Da / Density % sol: 40.71 %
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: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.15→33.98 Å / Num. all: 69492 / Num. obs: 69492 / % possible obs: 97.6 % / Redundancy: 2.5 % / Biso Wilson estimate: 9.06 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.047 / Rrim(I) all: 0.078 / Rsym value: 0.061 / Net I/σ(I): 7.4 / Num. measured all: 172082
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.5 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.15-1.210.4232497399870.7930.0190.0310.024296.7
3.64-33.980.024546822210.9990.0220.0360.02817.695.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.15 Å33.79 Å
Translation1.15 Å33.79 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
MOSFLMdata reduction
SCALA3.3.22data scaling
PHASER2.8.1phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TZF

4tzf


Resolution: 1.15→33.786 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1957 3523 5.07 %
Rwork0.167 65929 -
obs0.1684 69452 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 53.96 Å2 / Biso mean: 14.9127 Å2 / Biso min: 5.64 Å2
Refinement stepCycle: final / Resolution: 1.15→33.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 33 303 2037
Biso mean--11.82 29.41 -
Num. residues----229
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.15-1.16580.2541430.24612608275196
1.1658-1.18240.25681210.22992593271496
1.1824-1.20010.2041390.21252633277297
1.2001-1.21880.27271160.21982610272697
1.2188-1.23880.27231320.24622622275497
1.2388-1.26020.21381390.1962606274597
1.2602-1.28310.21511310.19242626275797
1.2831-1.30780.31131620.2692621278397
1.3078-1.33440.21551540.18162608276297
1.3344-1.36350.19791550.1682625278098
1.3635-1.39520.21481350.1672653278898
1.3952-1.43010.18161390.15582610274998
1.4301-1.46870.19271310.1522675280698
1.4687-1.5120.20551420.14622639278198
1.512-1.56080.16441390.13562651279098
1.5608-1.61650.16111180.14052704282298
1.6165-1.68130.18181290.14142685281499
1.6813-1.75780.1741540.14692648280298
1.7578-1.85040.17311380.15312656279499
1.8504-1.96640.22011580.19372630278897
1.9664-2.11820.15541650.14812654281999
2.1182-2.33130.21851570.18872484264192
2.3313-2.66850.19761470.16372693284099
2.6685-3.36160.16711350.152827332868100
3.3616-33.80070.18561440.14812662280695

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