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- PDB-6lj2: Crystal structure of NDM-1 in complex with heterodimer of D-capto... -

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Basic information

Entry
Database: PDB / ID: 6lj2
TitleCrystal structure of NDM-1 in complex with heterodimer of D-captopril derivative wss02127 stereoisomer
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 / beta-lactamase activity / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-EEX / Chem-EKX / HYDROXIDE ION / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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)26,3386
Polymers25,6321
Non-polymers7075
Water5,044280
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)41.799, 60.296, 42.426
Angle α, β, γ (deg.)90.000, 98.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 285 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO
#4: 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: isolated from a genetically manipulated source
Formula: C14H17NO3S
#5: Chemical ChemComp-EKX / (1S)-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: isolated from a genetically manipulated source
Formula: C14H17NO3S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 40.44 % / Mosaicity: 1.036 ° / Mosaicity esd: 0.012 °
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: 1.35→50 Å / Num. obs: 43712 / % possible obs: 95.5 % / Redundancy: 6.3 % / Biso Wilson estimate: 13.72 Å2 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.019 / Rrim(I) all: 0.05 / Χ2: 0.798 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.35-1.46.30.74643630.7910.3210.8140.83896.1
1.4-1.456.20.56944290.8610.2470.6220.84397.2
1.45-1.526.20.36244480.9190.1570.3960.89597.5
1.52-1.65.70.23443430.9460.1050.2570.8195
1.6-1.76.60.14644690.9780.0610.1580.74497.7
1.7-1.836.60.08644950.9880.0350.0930.72398.7
1.83-2.0260.06344310.9770.0280.071.04297.1
2.02-2.315.80.03238060.990.0140.0350.68882.8
2.31-2.9170.02345730.9950.0090.0250.73499.4
2.91-506.50.01643550.9960.0070.0170.68193.3

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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: 1.35→50 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.08
RfactorNum. reflection% reflection
Rfree0.1885 2097 4.95 %
Rwork0.1516 --
obs0.1535 42348 92.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.33 Å2 / Biso mean: 24.4677 Å2 / Biso min: 8.81 Å2
Refinement stepCycle: final / Resolution: 1.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 41 280 2022
Biso mean--29.2 36.15 -
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 (%)
1.35-1.37930.23441030.1692192066
1.3793-1.41380.22241260.1651247185
1.4138-1.4520.26081420.1723265892
1.452-1.49470.22941280.1727279995
1.4947-1.5430.19451600.1486276596
1.543-1.59810.2221210.141274693
1.5981-1.66210.20421530.1366281497
1.6621-1.73770.19631500.1379286899
1.7377-1.82930.18651640.1386286499
1.8293-1.94390.21721290.1966277895
1.9439-2.0940.18521720.1406286299
2.094-2.30470.20681010.1615218875
2.3047-2.63810.18631680.1501289599
2.6381-3.32330.20141460.1513290899
3.3233-500.14281340.143271591

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