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- PDB-6lj1: Crystal structure of NDM-1 in complex with D-captopril derivative... -

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Basic information

Entry
Database: PDB / ID: 6lj1
TitleCrystal structure of NDM-1 in complex with D-captopril derivative wss02127 monomer
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-EEX / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.151 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)26,0424
Polymers25,6321
Non-polymers4103
Water5,747319
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)40.795, 59.210, 42.041
Angle α, β, γ (deg.)90.000, 93.410, 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EEX / (1R)-2-[(2S)-2-methyl-3-sulfanyl-propanoyl]-3,4-dihydro-1H-isoquinoline-1-carboxylic acid


Mass: 279.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17NO3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 1.98 Å3/Da / Density % sol: 37.8 % / Mosaicity: 1.155 ° / Mosaicity esd: 0.01 °
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: BL17U1 / Wavelength: 0.97891 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 22, 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: 1.15→50 Å / Num. obs: 68710 / % possible obs: 97.2 % / Redundancy: 5.3 % / Biso Wilson estimate: 15.95 Å2 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.026 / Rrim(I) all: 0.062 / Χ2: 0.834 / Net I/σ(I): 9.3 / Num. measured all: 362094
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.15-1.194.30.79564530.7290.3880.890.80991.6
1.19-1.244.90.68368630.7950.3280.7620.79397.3
1.24-1.350.52367500.8610.2540.5840.80296.8
1.3-1.365.30.35268870.9150.1680.3920.84997.4
1.36-1.455.50.23269810.9470.1090.2580.8798.8
1.45-1.565.40.14368550.970.0680.1590.91797.2
1.56-1.725.50.08568730.9830.040.0950.89397.7
1.72-1.975.70.05269990.990.0240.0580.88499
1.97-2.485.40.03569500.9940.0160.0380.81997.7
2.48-505.60.02670990.9960.0110.0280.69898.9

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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: 1.151→50 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 18.28
RfactorNum. reflection% reflection
Rfree0.1604 3152 5.08 %
Rwork0.1397 --
obs0.1408 62106 87.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.88 Å2 / Biso mean: 22.7627 Å2 / Biso min: 11.96 Å2
Refinement stepCycle: final / Resolution: 1.151→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 21 319 2041
Biso mean--23.48 38.71 -
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 (%)
1.1512-1.16840.2343470.2077102335
1.1684-1.18660.251550.2172130145
1.1866-1.20610.28231070.2231163356
1.2061-1.22690.25751040.2419201971
1.2269-1.24920.24671310.2313229079
1.2492-1.27320.25941460.2267245284
1.2732-1.29920.23931470.2204248787
1.2992-1.32740.23971290.215271593
1.3274-1.35830.21981830.2022287298
1.3583-1.39230.21571590.1907281398
1.3923-1.42990.19871450.1765289298
1.4299-1.4720.16431490.1698285198
1.472-1.51950.19491710.1551282398
1.5195-1.57380.17571690.1473275095
1.5738-1.63690.16571480.1415281597
1.6369-1.71140.16931330.13752928100
1.7114-1.80160.16171630.1329287099
1.8016-1.91450.15691390.1294291399
1.9145-2.06230.13131290.1281288898
2.0623-2.26980.15151180.1265284396
2.2698-2.59820.16491660.13532911100
2.5982-3.27320.14211520.13172948100
3.2732-500.14121620.1238291798
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)
11.0470.6112-0.08142.66280.62341.5834-0.0093-0.10150.10160.11640.1187-0.0771-0.15740.1026-0.11830.1195-0.00220.00640.1768-0.02290.147835.590333.875440.7483
20.5094-0.1386-0.10880.59270.09880.65640.0033-0.00630.05160.00090.0179-0.0451-0.03080.0724-0.01520.1175-0.00150.00110.16-0.00280.151637.873325.24328.0251
32.3857-1.60980.15424.7826-1.6962.6205-0.1124-0.04660.14760.11970.10790.0162-0.1241-0.1374-0.00490.0926-0.0062-0.0150.1605-0.01980.127223.681132.791330.4125
41.7232-0.16140.14791.61030.01851.6555-0.00550.02690.099-0.0493-0.00950.0613-0.107-0.02520.00640.11140.00880.00460.16250.00120.166819.66531.621226.2958
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 42:70)A42 - 70
2X-RAY DIFFRACTION2(chain A and resid 71:198)A71 - 198
3X-RAY DIFFRACTION3(chain A and resid 199:221)A199 - 221
4X-RAY DIFFRACTION4(chain A and resid 222:270)A222 - 270

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