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- PDB-6ny7: Crystal Structure of NDM-1 D199N with Compound 16 -

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Basic information

Entry
Database: PDB / ID: 6ny7
TitleCrystal Structure of NDM-1 D199N with Compound 16
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 / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Chem-L8J / Metallo-beta-lactamase type 2 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 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 11, 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

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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)25,1294
Polymers24,6021
Non-polymers5283
Water5,242291
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)41.571, 59.774, 42.531
Angle α, β, γ (deg.)90.000, 97.880, 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, 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-L8J / [(5,7-dibromo-2-oxo-1,2-dihydroquinolin-4-yl)methyl]phosphonic acid


Mass: 396.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H8Br2NO4P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.13 Å3/Da / Density % sol: 42.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.05 M potassium phosphate (Dibasic), 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: Oct 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 40507 / % possible obs: 99.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.032 / Rrim(I) all: 0.062 / Χ2: 1.113 / Net I/σ(I): 12.6 / Num. measured all: 145939
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.422.80.55420040.6250.40.6870.76498.1
1.42-1.453.10.47719710.7610.3250.5790.84598.4
1.45-1.483.30.41620070.8080.2680.4960.91399.2
1.48-1.513.60.37320100.8780.2270.4370.93399.3
1.51-1.543.60.320000.9050.1830.3520.98699.2
1.54-1.583.70.26720510.9270.1610.3120.97699.8
1.58-1.623.70.23620000.9410.1420.2761.01799.5
1.62-1.663.70.19620350.9580.1180.2291.0599.7
1.66-1.713.70.16920090.9660.1020.1971.11399.8
1.71-1.763.70.13920250.9770.0840.1631.11299.9
1.76-1.833.70.11420230.9850.0690.1331.14399.9
1.83-1.93.70.09220280.990.0560.1081.249100
1.9-1.993.70.07520480.9920.0450.0881.35599.9
1.99-2.093.70.06120230.9950.0370.0711.37199.9
2.09-2.223.70.05420300.9960.0320.0631.222100
2.22-2.393.70.04720270.9970.0280.0551.24399.8
2.39-2.633.70.04220540.9980.0250.0491.22399.9
2.63-3.023.70.03720430.9980.0220.0441.224100
3.02-3.83.70.03220470.9980.0190.0371.08299.9
3.8-503.60.03320720.9980.020.0381.18898.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.2 Å25.07 Å
Translation5.2 Å25.07 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: 1.4→25.07 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.97
RfactorNum. reflection% reflection
Rfree0.1749 1996 4.93 %
Rwork0.1444 --
obs0.1459 40486 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 67.16 Å2 / Biso mean: 19.061 Å2 / Biso min: 6.94 Å2
Refinement stepCycle: final / Resolution: 1.4→25.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 20 292 2013
Biso mean--32.57 30.85 -
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 (%)
1.3995-1.43450.2391450.21262655280097
1.4345-1.47320.22591420.16762741288399
1.4732-1.51660.21471410.14932724286599
1.5166-1.56550.18551450.13792730287599
1.5655-1.62150.2311400.13727402880100
1.6215-1.68640.20471410.135727502891100
1.6864-1.76310.17531390.131427662905100
1.7631-1.8560.18271440.132927492893100
1.856-1.97230.17461490.125827522901100
1.9723-2.12450.16331430.126627692912100
2.1245-2.33810.15851400.136927472887100
2.3381-2.67610.16831380.14627712909100
2.6761-3.37040.16131390.155127832922100
3.3704-25.07410.16581500.15082813296399

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