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- PDB-6j8r: Metallo-Beta-Lactamase VIM-2 in complex with Dual MBL/SBL Inhibit... -

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Basic information

Entry
Database: PDB / ID: 6j8r
TitleMetallo-Beta-Lactamase VIM-2 in complex with Dual MBL/SBL Inhibitor MS01
ComponentsBeta-lactamase class B VIM-2
KeywordsHYDROLASE / Metallo-beta-lactamase VIM-2 / VIM-2
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / periplasmic space / hydrolase activity / response to antibiotic / metal 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-BHU / FORMIC ACID / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.575 Å
AuthorsLi, G.-B. / Liu, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81874291; 81502989 China
CitationJournal: J.Med.Chem. / Year: 2019
Title: Structure-Based Development of (1-(3'-Mercaptopropanamido)methyl)boronic Acid Derived Broad-Spectrum, Dual-Action Inhibitors of Metallo- and Serine-beta-lactamases.
Authors: Wang, Y.L. / Liu, S. / Yu, Z.J. / Lei, Y. / Huang, M.Y. / Yan, Y.H. / Ma, Q. / Zheng, Y. / Deng, H. / Sun, Y. / Wu, C. / Yu, Y. / Chen, Q. / Wang, Z. / Wu, Y. / Li, G.B.
History
DepositionJan 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _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

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,58614
Polymers24,6791
Non-polymers90613
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-0 kcal/mol
Surface area9450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.893, 60.984, 96.338
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase class B VIM-2 / BlaVIM-2 / Metallo beta-lactamase / Metallo-beta-lactamase VIM-2 / Subclass B1 metallo-beta- ...BlaVIM-2 / Metallo beta-lactamase / Metallo-beta-lactamase VIM-2 / Subclass B1 metallo-beta-lactamase VIM-2 / VIM-2 / VIM-2 beta-lactamase / VIM-2 class B metallo b-lactamase / VIM-2 metallo-beta-lactamase / VIM-2 type metallo-beta-lactamase


Mass: 24679.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, VIM-2, vim-2, IPC669_36195
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K2N0

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Non-polymers , 5 types, 236 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BHU / [[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]methylboronic acid / (S)-((3-mercapto-2-methylpropanamido)methyl)boronic acid


Mass: 177.030 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12BNO3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Magnesium Formate, 21%-27% (v/v) Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 195 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Jun 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 36585 / % possible obs: 99.8 % / Redundancy: 12.3 % / Biso Wilson estimate: 13.63 Å2 / Rmerge(I) obs: 0.254 / Rpim(I) all: 0.073 / Rrim(I) all: 0.264 / Χ2: 0.957 / Net I/σ(I): 5.8 / Num. measured all: 401008
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.57-1.6910.30.83721010.7090.2680.8810.66598.9
1.69-1.7311.10.76121530.7820.2350.7980.7399.2
1.73-1.7811.70.68621350.8160.2070.7170.7999.7
1.78-1.8311.60.58321360.8480.1770.610.8599.7
1.83-1.8911.50.51121480.8950.1540.5340.93699.8
1.89-1.9612.20.48521440.9090.1410.5051.04699.8
1.96-2.03130.44321660.9030.1250.4611.10899.8
2.03-2.13130.41121430.9290.1160.4271.18499.8
2.13-2.24130.38821750.9390.1110.4041.18100
2.24-2.3812.40.3621780.940.1050.3751.186100
2.38-2.5612.90.33221840.950.0940.3451.139100
2.56-2.8213.40.30221990.9590.0840.3131.051100
2.82-3.2312.90.26722060.9820.0760.2780.913100
3.23-4.0712.50.24422400.9760.070.2540.827100
4.07-5012.20.20423770.9790.0590.2130.629100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.27 Å48.17 Å
Translation6.27 Å48.17 Å

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Processing

Software
NameVersionClassificationNB
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.6.0phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LCA

5lca


Resolution: 1.575→48.169 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1765 2000 5.47 %
Rwork0.152 34584 -
obs0.1534 36584 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.76 Å2 / Biso mean: 18.1487 Å2 / Biso min: 5.76 Å2
Refinement stepCycle: final / Resolution: 1.575→48.169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1733 0 55 232 2020
Biso mean--28.33 29.91 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081841
X-RAY DIFFRACTIONf_angle_d0.9572492
X-RAY DIFFRACTIONf_chiral_restr0.056283
X-RAY DIFFRACTIONf_plane_restr0.006326
X-RAY DIFFRACTIONf_dihedral_angle_d15.7991060
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5749-1.61420.2781090.23491885199475
1.6142-1.65790.25921370.22122357249495
1.6579-1.70670.2661410.19512453259499
1.7067-1.76180.22161440.176424932637100
1.7618-1.82470.17281430.168824782621100
1.8247-1.89780.20171460.156825092655100
1.8978-1.98420.17971430.152324822625100
1.9842-2.08880.16641450.140725172662100
2.0888-2.21970.14351470.135425162663100
2.2197-2.3910.17811450.129925172662100
2.391-2.63160.17151470.138725422689100
2.6316-3.01240.14941480.135325592707100
3.0124-3.79510.15781490.134425772726100
3.7951-48.19150.17551560.16626992855100

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