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- PDB-6o3r: Crystal Structure of NDM-1 D199N with Compound 7 -

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Basic information

Entry
Database: PDB / ID: 6o3r
TitleCrystal Structure of NDM-1 D199N with Compound 7
ComponentsCarbapenem Hydrolyzing Class B Metallo beta lactamase NDM-1
KeywordsHYDROLASE / Carbapenemase / Phosphonate / inhibitor / complex
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding / metal 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-XJE / Metallo-beta-lactamase type 2 / NDM-1
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 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)Al103158 United States
CitationJournal: J.Med.Chem. / Year: 2019
Title: Heteroaryl Phosphonates as Noncovalent Inhibitors of Both Serine- and Metallocarbapenemases.
Authors: Pemberton, O.A. / Jaishankar, P. / Akhtar, A. / Adams, J.L. / Shaw, L.N. / Renslo, A.R. / Chen, Y.
History
DepositionFeb 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
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: Carbapenem Hydrolyzing Class B Metallo beta lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0174
Polymers24,6021
Non-polymers4153
Water5,332296
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)41.663, 60.219, 42.504
Angle α, β, γ (deg.)90.000, 97.980, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbapenem Hydrolyzing Class B Metallo beta lactamase NDM-1 / Metallo beta-lactamase / Metallo-beta-lactamase NDM-1 / NDM-1 metallo-beta-lactamase / NDM1 metallo- ...Metallo beta-lactamase / Metallo-beta-lactamase NDM-1 / NDM-1 metallo-beta-lactamase / NDM1 metallo-beta-lactamase / New Delhi Metallo carbapenemase-1 / New Delhi metallo-beta-lactamase NDM-1 / New Delhi metallo-beta-lactamse 1 / Subclass B1 metallo-beta-lactamase NDM-1


Mass: 24601.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: blaNDM-1, bla NDM-1, blaNDM-1_1, blaNDM-1_2, blaNDM-1_3, blaNDM1, NDM-1, C3483_29595, C7V41_28630, D647_p47098, DDJ63_29735, DZB15_28435, EC13450_007, NCTC13443_00040, p2146_00143, pCRE380_21, ...Gene: blaNDM-1, bla NDM-1, blaNDM-1_1, blaNDM-1_2, blaNDM-1_3, blaNDM1, NDM-1, C3483_29595, C7V41_28630, D647_p47098, DDJ63_29735, DZB15_28435, EC13450_007, NCTC13443_00040, p2146_00143, pCRE380_21, PMK1_ndm00067, PMK1_ndm00076, PMK1_ndm00085, pN11x00042NDM_090, pNDM-SX04_5, pNDM10469_138, SAMEA3531848_05178, SAMEA4394746_03823, TR3_031, TR4_031
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E9NWK5, UniProt: C7C422*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-XJE / [(5-methoxy-7-methyl-2-oxo-2H-1-benzopyran-4-yl)methyl]phosphonic acid


Mass: 284.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H13O6P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.15 Å3/Da / Density % sol: 42.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.05 M Potassium Phosphate (Di Basic), 0.01 M Calcium Chloride, 25%(w/v) PEG-8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 51215 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.026 / Rrim(I) all: 0.05 / Χ2: 0.91 / Net I/σ(I): 11.9 / Num. measured all: 188121
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.3-1.3230.26925200.9180.1840.3280.87599.8
1.32-1.353.20.25625520.9170.170.3080.866100
1.35-1.373.30.23825640.9340.1530.2830.913100
1.37-1.43.70.2225360.9520.1340.2580.977100
1.4-1.433.80.20225510.9590.1220.2360.936100
1.43-1.463.80.17725650.9690.1060.2070.992100
1.46-1.53.80.15125410.9770.0910.1770.995100
1.5-1.543.80.13125740.980.0790.1530.992100
1.54-1.593.80.11425530.9840.0690.1340.99100
1.59-1.643.80.10225670.9880.0610.1190.974100
1.64-1.73.80.08825440.9890.0530.1020.967100
1.7-1.763.80.07525580.9920.0450.0880.975100
1.76-1.843.80.06425640.9940.0390.0750.963100
1.84-1.943.80.05325760.9950.0320.0620.977100
1.94-2.063.80.04625310.9960.0280.0540.95100
2.06-2.223.80.04225890.9960.0250.0490.921100
2.22-2.453.80.03825690.9970.0230.0440.878100
2.45-2.83.80.03325760.9980.020.0390.784100
2.8-3.533.80.02726030.9980.0160.0320.665100
3.53-503.60.02325820.9980.0150.0280.56398.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.21 Å21.85 Å
Translation5.21 Å21.85 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3228refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TZF

4tzf


Resolution: 1.3→21.848 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.26
RfactorNum. reflection% reflection
Rfree0.1807 1989 3.94 %
Rwork0.1531 --
obs0.1542 50489 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.64 Å2 / Biso mean: 19.6859 Å2 / Biso min: 8.92 Å2
Refinement stepCycle: final / Resolution: 1.3→21.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 21 296 2018
Biso mean--18.14 31.71 -
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 (%)
1.2982-1.33070.21841140.16982833294781
1.3307-1.36670.22731400.16183405354597
1.3667-1.40690.19931480.155434893637100
1.4069-1.45230.20291410.148434973638100
1.4523-1.50420.17961410.137235233664100
1.5042-1.56440.1641430.131535143657100
1.5644-1.63550.1511470.1335283675100
1.6355-1.72170.18861450.134835033648100
1.7217-1.82960.15871420.140635233665100
1.8296-1.97070.18561460.137935063652100
1.9707-2.16890.16481480.145335323680100
2.1689-2.48240.17841440.157735303674100
2.4824-3.12610.18551460.171435353681100
3.1261-21.85090.18411440.15933582372699

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