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- PDB-5zj2: Crystal structure of NDM-1 in complex with D-captopril -

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Basic information

Entry
Database: PDB / ID: 5zj2
TitleCrystal structure of NDM-1 in complex with D-captopril
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE / NDM-1 / metallo-beta-lactamase / antibiotic resistent / inhibitor / thio compounds
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-MCO / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsZhang, H. / Hao, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)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
DepositionMar 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
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)25,9804
Polymers25,6321
Non-polymers3483
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-56 kcal/mol
Surface area9750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.698, 59.892, 42.138
Angle α, β, γ (deg.)90.000, 97.780, 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) / Strain (production host): BL21(DE3) / 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-MCO / 1-(3-MERCAPTO-2-METHYL-PROPIONYL)-PYRROLIDINE-2-CARBOXYLIC ACID


Mass: 217.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15NO3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O

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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: 2.03 Å3/Da / Density % sol: 39.53 % / Mosaicity: 0.209 ° / 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
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2016
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 82705 / % possible obs: 99.7 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.042 / Rrim(I) all: 0.091 / Χ2: 0.895 / Net I/σ(I): 10 / Num. measured all: 395792
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.1-1.144.60.67182210.7650.3540.7610.937100
1.14-1.184.70.52482610.8410.2720.5920.964100
1.18-1.244.80.40582900.8940.2090.4570.976100
1.24-1.34.80.3182820.9340.1590.350.929100
1.3-1.394.80.22482580.9580.1150.2530.88100
1.39-1.494.80.16282950.9730.0820.1820.8999.9
1.49-1.644.90.12282470.9790.0610.1371.00199.8
1.64-1.884.90.08782930.9880.0440.0980.93299.7
1.88-2.374.90.06283020.9920.0310.070.72499.7
2.37-504.70.05782560.990.0320.0660.72697.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q6X

3q6x
PDB Unreleased entry


Resolution: 1.1→27.95 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / WRfactor Rfree: 0.1644 / WRfactor Rwork: 0.1371 / FOM work R set: 0.8899 / SU B: 1.098 / SU ML: 0.023 / SU R Cruickshank DPI: 0.03 / SU Rfree: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1616 3859 5 %RANDOM
Rwork0.1355 ---
obs0.1368 73459 93.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 74.56 Å2 / Biso mean: 23.137 Å2 / Biso min: 10.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.48 Å2
2---0.41 Å20 Å2
3---0.47 Å2
Refinement stepCycle: final / Resolution: 1.1→27.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 16 294 2011
Biso mean--25.28 37.78 -
Num. residues----229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0151807
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171607
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.7442471
X-RAY DIFFRACTIONr_angle_other_deg0.6351.7223761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8465243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.12520.31264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97415246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.676159
X-RAY DIFFRACTIONr_chiral_restr0.3550.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212106
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02338
X-RAY DIFFRACTIONr_rigid_bond_restr3.30233414
X-RAY DIFFRACTIONr_sphericity_free28.7135185
X-RAY DIFFRACTIONr_sphericity_bonded10.60153477
LS refinement shellResolution: 1.101→1.129 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 155 -
Rwork0.215 2846 -
all-3001 -
obs--49.11 %
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)
17.0937-5.1211-8.56015.08216.529711.74-0.46770.3816-0.4671.0293-0.16130.35030.4764-0.6020.62910.45150.01060.00120.18350.02480.058434.803933.95647.6209
21.43950.7769-0.52834.99990.27241.30490.0629-0.14590.154-0.0095-0.0790.2078-0.131-0.00670.01610.0697-0.02240.03280.1187-0.04150.060932.67334.118239.0774
30.50030.2637-0.27561.82660.061.40340.007-0.071-0.0178-0.1563-0.11480.03980.0531-0.00790.10780.03970.01120.01630.0672-0.00610.041135.73525.483528.2323
42.77543.19292.330912.0908-2.71885.49-0.8818-0.2760.8221-0.58230.0880.6117-1.1532-0.35320.79380.5766-0.1581-0.05690.3679-0.33660.45119.364640.258428.7574
53.25-0.6225-0.19341.225-0.15831.12150.08220.16740.255-0.16980.03420.45450.007-0.2447-0.11640.02450.0052-0.06630.12450.02010.259319.126330.55126.015
612.20446.6194-6.237110.7042-3.494913.90880.09251.22930.9966-0.83630.46690.42440.0779-0.6374-0.55940.34020.119-0.03970.23620.160.183213.533737.84517.1572
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 46
2X-RAY DIFFRACTION2A47 - 70
3X-RAY DIFFRACTION3A71 - 210
4X-RAY DIFFRACTION4A211 - 220
5X-RAY DIFFRACTION5A221 - 265
6X-RAY DIFFRACTION6A266 - 270

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