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- PDB-6lj0: Crystal structure of NDM-1 in complex with D-captopril derivative... -

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Basic information

Entry
Database: PDB / ID: 6lj0
TitleCrystal structure of NDM-1 in complex with D-captopril derivative wss02122
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 / 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-EER / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,9944
Polymers25,6321
Non-polymers3623
Water5,260292
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)41.818, 60.060, 42.169
Angle α, β, γ (deg.)90.000, 98.060, 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-EER / (2R)-1-[(2S)-2-methyl-3-sulfanyl-propanoyl]piperidine-2-carboxylic acid


Mass: 231.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17NO3S / 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.: 292 / 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: 2.05 Å3/Da / Density % sol: 39.87 % / Mosaicity: 0.492 ° / Mosaicity esd: 0.004 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M Bis-Tris pH5.5, 15% PEG3350, 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: 0.97891 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2018
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 63815 / % possible obs: 98.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 14.57 Å2 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.017 / Rrim(I) all: 0.043 / Χ2: 0.896 / Net I/σ(I): 12.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.2-1.246.40.74763960.810.3210.8150.91599.1
1.24-1.296.20.54462940.8720.2350.5940.91398.1
1.29-1.356.30.36262530.9320.1560.3950.91996.7
1.35-1.426.60.24863930.9630.1050.270.88699.5
1.42-1.516.60.14864270.9840.0620.1610.83998.9
1.51-1.636.30.08762500.990.0370.0950.80496.5
1.63-1.796.90.05664440.9950.0230.0610.82999.8
1.79-2.056.70.03864400.9960.0150.0410.93899.4
2.05-2.596.50.02963780.9970.0120.0310.97998
2.59-506.80.02665400.9970.0110.0280.93498.8

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XP6

5xp6


Resolution: 1.2→50 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 17.61
RfactorNum. reflection% reflection
Rfree0.1738 3104 5.08 %
Rwork0.1527 --
obs0.1538 61049 94.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.61 Å2 / Biso mean: 25.409 Å2 / Biso min: 9.29 Å2
Refinement stepCycle: final / Resolution: 1.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 17 292 2010
Biso mean--29.35 39.26 -
Num. residues----229
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2-1.21620.2767690.2405136750
1.2162-1.23620.2471220.2324201873
1.2362-1.25750.2461300.2179236185
1.2575-1.28030.21321550.2064261694
1.2803-1.3050.18751350.1999260693
1.305-1.33160.23971470.1894264196
1.3316-1.36060.20471560.18982804100
1.3606-1.39220.20681540.1837274099
1.3922-1.4270.19771450.1818276299
1.427-1.46560.1941700.1683275899
1.4656-1.50870.20551490.1671276398
1.5087-1.55740.18681580.1674270597
1.5574-1.61310.17881580.1563263895
1.6131-1.67770.16531250.15132824100
1.6777-1.75410.19161470.14982783100
1.7541-1.84650.18861550.15052785100
1.8465-1.96220.19041400.15132776100
1.9622-2.11370.15771070.1466282598
2.1137-2.32640.19051390.1475273097
2.3264-2.6630.15231470.15242793100
2.663-3.35490.16481430.1458281999
3.3549-500.15071530.1359283198
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.41810.28140.05973.65290.46970.9880.0113-0.16820.17820.1558-0.06250.1129-0.19540.02480.0150.1474-0.0210.04130.1552-0.04020.133833.327834.120640.4464
20.51070.1735-0.27111.78250.16961.9187-0.0064-0.02780.0044-0.1024-0.07180.01120.011-0.0140.06580.07930.00850.01560.1125-0.01120.122835.960725.658428.4358
30.0712-0.31710.05191.5316-0.54370.8533-0.004-0.16290.16060.24340.20290.2663-0.2577-0.1575-0.17820.34730.2109-0.01110.4605-0.09860.653520.358840.877327.0912
40.94730.4255-0.3710.6010.17490.4304-0.00550.17970.2097-0.0911-0.05610.4562-0.0846-0.4726-0.35070.14020.0516-0.03740.3626-0.06690.372319.834930.4626.0194
56.0432-0.77582.03162.7480.24940.78120.15880.43190.415-0.4875-0.16970.5709-0.3621-0.48920.01780.39520.238-0.11320.62740.08330.690314.448338.462418.8081
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 42:70)A42 - 70
2X-RAY DIFFRACTION2(chain A and resseq 71:210)A71 - 210
3X-RAY DIFFRACTION3(chain A and resseq 211:221)A211 - 221
4X-RAY DIFFRACTION4(chain A and resseq 222:262)A222 - 262
5X-RAY DIFFRACTION5(chain A and resseq 263:270)A263 - 270

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