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- PDB-6lj5: Crystal structure of NDM-1 in complex with D-captopril derivative... -

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Basic information

Entry
Database: PDB / ID: 6lj5
TitleCrystal structure of NDM-1 in complex with D-captopril derivative wss04145
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-EF0 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 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)26,0565
Polymers25,6321
Non-polymers4244
Water4,774265
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)41.785, 60.015, 42.321
Angle α, β, γ (deg.)90.000, 98.480, 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-EF0 / 1-[(2S)-2-methyl-3-sulfanyl-propanoyl]piperidine-4-carboxylic acid


Mass: 231.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17NO3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 265 / 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: 39.93 % / Mosaicity: 0.569 ° / Mosaicity esd: 0.005 °
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: 1.26→50 Å / Num. obs: 53699 / % possible obs: 96.3 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.026 / Rrim(I) all: 0.066 / Χ2: 1.48 / Net I/σ(I): 12 / Num. measured all: 352156
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.26-1.316.60.79555610.8310.3350.8650.64499.5
1.31-1.366.60.51354600.9190.2160.5580.55798.9
1.36-1.426.50.36154310.9480.1530.3930.6198.2
1.42-1.496.50.23954160.9770.1010.260.71897.3
1.49-1.596.90.16255510.9860.0670.1760.90999.9
1.59-1.716.80.11755230.9910.0490.1271.22599.4
1.71-1.886.60.08554880.9940.0360.0921.77198.4
1.88-2.156.30.06248050.9970.0270.0682.71186.4
2.15-2.716.50.05250030.9970.0220.0573.08989.5
2.71-506.20.0454610.9990.0170.0443.07196.1

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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: 1.26→24.39 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 15.4
RfactorNum. reflection% reflection
Rfree0.1664 2724 5.07 %
Rwork0.1351 --
obs0.1368 53676 96.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.73 Å2 / Biso mean: 23.6045 Å2 / Biso min: 8.97 Å2
Refinement stepCycle: final / Resolution: 1.26→24.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 21 265 1987
Biso mean--40.32 38.7 -
Num. residues----229
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.26-1.280.21581520.17132734288698
1.28-1.310.23771340.19512795292999
1.31-1.330.19651350.16292746288199
1.33-1.360.20291660.15332720288699
1.36-1.40.19661490.14412702285198
1.4-1.430.17721350.1352711284697
1.43-1.470.14371380.12812662280096
1.47-1.510.16021890.123227422931100
1.51-1.560.16141180.122728122930100
1.56-1.620.17821380.122227752913100
1.62-1.680.1371310.11782769290099
1.68-1.760.15851460.11942763290999
1.76-1.850.14791120.12712749286198
1.85-1.970.15391170.13852079219675
1.97-2.120.16921440.13142762290698
2.12-2.330.1621250.14332226235180
2.33-2.670.1631680.143827662934100
2.67-3.360.18911760.13882754293099
3.36-24.390.14721510.12882685283694

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