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- PDB-6lj7: Crystal structure of NDM-1 in complex with D-captopril derivative... -

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Basic information

Entry
Database: PDB / ID: 6lj7
TitleCrystal structure of NDM-1 in complex with D-captopril derivative wss05010
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE / NDM-1 / metallo-beta-lactamase / antibiotic resistent / inhibitor / thio compounds / ANTIBIOTIC
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-EFR / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsZhang, H. / Ma, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670753 China
CitationJournal: Bioorg.Med.Chem. / Year: 2020
Title: Structure-guided optimization of D-captopril for discovery of potent NDM-1 inhibitors.
Authors: Ma, G. / Wang, S. / Wu, K. / Zhang, W. / Ahmad, A. / Hao, Q. / Lei, X. / Zhang, H.
History
DepositionDec 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 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)26,0074
Polymers25,6321
Non-polymers3753
Water6,557364
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.851, 60.158, 42.530
Angle α, β, γ (deg.)90.000, 98.470, 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: 25631.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Plasmid: pRHisMBP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C7C422, beta-lactamase
#2: Chemical ChemComp-EFR / 2-[1-[(2S)-2-methyl-3-sulfanyl-propanoyl]piperidin-4-yl]ethanamide


Mass: 244.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20N2O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.07 Å3/Da / Density % sol: 40.46 % / Mosaicity: 0.297 ° / Mosaicity esd: 0.003 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M Bis-Tris pH5.5, 15% PEG 3350, 20mM L-proline

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97894 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2018
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97894 Å / Relative weight: 1
ReflectionResolution: 1.16→50 Å / Num. obs: 69433 / % possible obs: 96 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.028 / Rrim(I) all: 0.069 / Χ2: 2.063 / Net I/σ(I): 14.4 / Num. measured all: 431892
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.16-1.24.80.31558000.9340.1590.3550.69180.8
1.2-1.256.20.25870610.9630.110.2810.84597.9
1.25-1.316.70.20871430.9770.0860.2261.02599.2
1.31-1.386.60.16171020.9840.0670.1751.17798.6
1.38-1.466.20.12570370.9880.0540.1371.46897.7
1.46-1.576.90.09671850.9940.0390.1041.98499.4
1.57-1.736.70.0871390.9940.0330.0862.61699
1.73-1.9860.06370300.9960.0280.073.34897
1.98-2.56.30.05372220.9970.0230.0583.63399.6
2.5-505.60.04767140.9970.0220.0523.65491.2

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHENIX1.13refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XP6

5xp6


Resolution: 1.16→24.33 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 13.28
RfactorNum. reflection% reflection
Rfree0.1609 3467 5 %
Rwork0.1415 --
obs0.1424 69408 95.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 59.69 Å2 / Biso mean: 17.4834 Å2 / Biso min: 6.34 Å2
Refinement stepCycle: final / Resolution: 1.16→24.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 18 364 2083
Biso mean--13.96 32.95 -
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 (%)
1.16-1.170.2139940.15351974206873
1.17-1.190.16961070.14032292239983
1.19-1.210.15081420.1332470261291
1.21-1.230.15451530.13872730288399
1.23-1.250.17521220.13422708283099
1.25-1.270.15931330.1352728286199
1.27-1.290.16391430.13442719286299
1.29-1.320.15481510.1292700285199
1.32-1.340.171620.12542671283399
1.34-1.370.15171830.12112676285998
1.37-1.410.14291730.11582640281398
1.41-1.440.14861800.11862643282397
1.44-1.480.13831380.11752697283599
1.48-1.520.12261390.11422733287299
1.52-1.570.15691620.11082725288799
1.57-1.630.13241370.11692728286599
1.63-1.690.1499920.122765285799
1.69-1.770.18381400.13212725286598
1.77-1.860.15581190.13682660277997
1.86-1.980.16211480.14052658280696
1.98-2.130.15581510.145427432894100
2.13-2.350.17041170.149627722889100
2.35-2.690.16191200.16562769288999
2.69-3.380.1751490.15492692284197
3.39-24.330.1651120.15982323243582

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