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- PDB-6lj4: Crystal structure of NDM-1 in complex with D-captopril derivative... -

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Basic information

Entry
Database: PDB / ID: 6lj4
TitleCrystal structure of NDM-1 in complex with D-captopril derivative wss04146
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-EF9 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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)25,9944
Polymers25,6321
Non-polymers3623
Water4,756264
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)41.732, 60.054, 42.330
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EF9 / (3S)-1-[(2S)-2-methyl-3-sulfanyl-propanoyl]piperidine-3-carboxylic acid


Mass: 231.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17NO3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 39.97 % / Mosaicity: 0.39 ° / Mosaicity esd: 0.004 °
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: 1.15→50 Å / Num. obs: 70295 / % possible obs: 96 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.03 / Rrim(I) all: 0.075 / Χ2: 1.65 / Net I/σ(I): 11.3 / Num. measured all: 439120
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.15-1.194.50.76657130.7260.40.8670.51878.4
1.19-1.245.90.56870320.8730.2540.6240.59596.3
1.24-1.36.70.40872350.9360.170.4430.6499.2
1.3-1.366.70.27472290.9660.1150.2980.72198.9
1.36-1.456.30.19471330.9770.0830.2110.89797.8
1.45-1.566.90.1372640.9890.0530.141.30299.3
1.56-1.726.80.09872480.9920.0410.1061.85998.9
1.72-1.976.20.07171720.9950.0310.0782.72697.9
1.97-2.486.50.05673270.9970.0230.0613.38999.6
2.48-505.70.04669420.9970.0210.0513.54893.2

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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: 1.15→24.29 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.36
RfactorNum. reflection% reflection
Rfree0.1771 3504 4.99 %
Rwork0.1523 --
obs0.1535 70267 95.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 60.49 Å2 / Biso mean: 23.3252 Å2 / Biso min: 7.99 Å2
Refinement stepCycle: final / Resolution: 1.15→24.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1690 0 17 264 1971
Biso mean--33.48 36.82 -
Num. residues----228
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 (%)
1.15-1.170.2216900.21421980207071
1.17-1.180.23871190.21622213233280
1.18-1.20.21821260.19012447257387
1.2-1.220.20071480.18922664281297
1.22-1.240.21411300.18862744287499
1.24-1.260.21451420.17642768291099
1.26-1.280.20471350.17512791292699
1.28-1.310.2091480.16252736288499
1.31-1.330.19691660.16692734290099
1.33-1.360.18981780.16062699287799
1.36-1.40.16311780.14982670284898
1.4-1.430.16861830.14972718290199
1.43-1.470.17521450.1452702284797
1.47-1.510.18381340.1452772290699
1.51-1.560.18781680.14132732290099
1.56-1.620.17091470.13842762290999
1.62-1.680.1418950.13572793288899
1.68-1.760.16351340.1352773290799
1.76-1.850.16611270.13292736286398
1.85-1.970.15411520.13982708286097
1.97-2.120.14831500.13712787293799
2.12-2.330.15821210.144428022923100
2.33-2.670.16811230.15532801292499
2.67-3.360.19211500.15662769291998
3.36-24.290.1871150.16022462257786

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