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- PDB-6v1m: Structure of NDM-1 bound to QPX7728 at 1.05 A -

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Basic information

Entry
Database: PDB / ID: 6v1m
TitleStructure of NDM-1 bound to QPX7728 at 1.05 A
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE/HYDROLASE Inhibitor / carbapenemase / boronate / inhibitor / beta-lactamase / 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 / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Chem-QNA / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.05 Å
AuthorsPemberton, O.A. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Health & Human Services (HHS)HHSO100201600026C United States
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery of Cyclic Boronic Acid QPX7728, an Ultrabroad-Spectrum Inhibitor of Serine and Metallo-beta-lactamases.
Authors: Hecker, S.J. / Reddy, K.R. / Lomovskaya, O. / Griffith, D.C. / Rubio-Aparicio, D. / Nelson, K. / Tsivkovski, R. / Sun, D. / Sabet, M. / Tarazi, Z. / Parkinson, J. / Totrov, M. / Boyer, S.H. ...Authors: Hecker, S.J. / Reddy, K.R. / Lomovskaya, O. / Griffith, D.C. / Rubio-Aparicio, D. / Nelson, K. / Tsivkovski, R. / Sun, D. / Sabet, M. / Tarazi, Z. / Parkinson, J. / Totrov, M. / Boyer, S.H. / Glinka, T.W. / Pemberton, O.A. / Chen, Y. / Dudley, M.N.
History
DepositionNov 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 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)24,9724
Polymers24,6031
Non-polymers3703
Water5,621312
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)41.400, 60.240, 42.060
Angle α, β, γ (deg.)90.000, 98.460, 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-QNA / (1~{a}~{R},7~{b}~{S})-5-fluoranyl-2,2-bis(oxidanyl)-1~{a},7~{b}-dihydro-1~{H}-cyclopropa[c][1,2]benzoxaborinine-4-carboxylic acid


Mass: 238.985 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9BFO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 41.67 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 50 mM Potassium phosphate monobasic, 10 mM Calcium chloride, 25% (w/v) PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.05→27.98 Å / Num. obs: 94249 / % possible obs: 99.1 % / Redundancy: 3.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.2
Reflection shellResolution: 1.05→1.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.283 / Num. measured all: 14480 / Num. unique obs: 4572 / CC1/2: 0.921 / Net I/σ(I) obs: 3.9 / % possible all: 96.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.05 Å24.26 Å
Translation1.05 Å24.26 Å

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
PHASER2.8.0phasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
iMOSFLM7.2.2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TZF

4tzf


Resolution: 1.05→24.26 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 13.48
RfactorNum. reflection% reflection
Rfree0.1578 9162 4.95 %
Rwork0.1409 --
obs0.1418 94244 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 59.24 Å2 / Biso mean: 17.7128 Å2 / Biso min: 6.3 Å2
Refinement stepCycle: final / Resolution: 1.05→24.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1702 0 19 312 2033
Biso mean--12.71 35.39 -
Num. residues----229
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.05-1.060.2332950.21845191548687
1.06-1.070.21273110.202459536264100
1.07-1.090.21212620.189759956257100
1.09-1.10.19372990.170159276226100
1.1-1.120.18183160.163359786294100
1.12-1.130.1892920.163259456237100
1.13-1.150.16962960.1559496245100
1.15-1.160.16112900.147359886278100
1.16-1.180.1713320.152159316263100
1.18-1.20.17033160.143659186234100
1.2-1.220.14833600.137558676227100
1.22-1.240.15223160.136559456261100
1.24-1.270.13252840.132859776261100
1.27-1.290.14463180.129359706288100
1.29-1.320.14852520.127159916243100
1.32-1.350.13112730.119659746247100
1.35-1.390.13952950.124759516246100
1.39-1.430.11792910.122459676258100
1.43-1.470.12832780.125360036281100
1.47-1.510.13832850.122359116196100
1.51-1.570.13383590.123759146273100
1.57-1.630.14542780.125560156293100
1.63-1.710.13373700.124758876257100
1.71-1.80.14433420.127559126254100
1.8-1.910.14033000.128659406240100
1.91-2.050.14613200.133259286248100
2.06-2.260.14813630.13759116274100
2.26-2.590.1533090.145459576266100
2.59-3.260.18573330.14735808614199
3.26-24.260.19162270.16384500472775

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