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- PDB-7yhb: Crystal structure of VIM-2 MBL in complex with (2-(4-phenyl-1H-1,... -

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Basic information

Entry
Database: PDB / ID: 7yhb
TitleCrystal structure of VIM-2 MBL in complex with (2-(4-phenyl-1H-1,2,3-triazol-1-yl)benzyl)phosphonic acid
ComponentsBeta-lactamase class B VIM-2
KeywordsHYDROLASE/INHIBITOR / Metallo-Beta-lactamase class VIM-2 / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


hydrolase activity / metal 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-ITV / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.43 Å
AuthorsLi, G.-B. / Yan, Y.-H.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82122065 China
National Natural Science Foundation of China (NSFC)82073698 China
National Natural Science Foundation of China (NSFC)81874291 China
CitationJournal: Eur.J.Med.Chem. / Year: 2023
Title: Metal binding pharmacophore click-derived discovery of new broad-spectrum metallo-beta-lactamase inhibitors.
Authors: Yan, Y.H. / Ding, H.S. / Zhu, K.R. / Mu, B.S. / Zheng, Y. / Huang, M.Y. / Zhou, C. / Li, W.F. / Wang, Z. / Wu, Y. / Li, G.B.
History
DepositionJul 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,2518
Polymers49,3592
Non-polymers8926
Water3,909217
1
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1264
Polymers24,6791
Non-polymers4463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1264
Polymers24,6791
Non-polymers4463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.517, 79.293, 67.395
Angle α, β, γ (deg.)90.000, 130.160, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-lactamase class B VIM-2 / BlaVIM-2 / Metallo beta lactamase VIM-2 / Metallo beta-lactamase / Metallo-beta lactamase protein / ...BlaVIM-2 / Metallo beta lactamase VIM-2 / Metallo beta-lactamase / Metallo-beta lactamase protein / Metallo-beta-lactamase VIM-2 / VIM-2 class B 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.: 2
Source method: isolated from a genetically manipulated source
Details: Pseudomonas aeruginosa / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, blm, VIM-2, vim-2, PAERUG_P32_London_17_VIM_2_10_11_06255
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K2N0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ITV / [2-(4-phenyl-1,2,3-triazol-1-yl)phenyl]methylphosphonic acid


Mass: 315.264 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H14N3O3P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.08 Å3/Da / Density % sol: 40.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Magnesium Formate, 23-30% (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: 1 Å
DetectorType: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Dec 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.43→19.45 Å / Num. obs: 91708 / % possible obs: 96.62 % / Redundancy: 6 % / Biso Wilson estimate: 20.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Net I/σ(I): 8.1
Reflection shellResolution: 1.43→1.54 Å / Rmerge(I) obs: 0.891 / Num. unique obs: 14215

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.17 Å19.45 Å
Translation1.17 Å19.45 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1refinement
HKL-2000data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JN6

6jn6


Resolution: 1.43→19.093 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.6 / Phase error: 39.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3084 1458 2.01 %
Rwork0.2631 70922 -
obs0.264 72380 97.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 42.95 Å2 / Biso mean: 20.9388 Å2 / Biso min: 0.51 Å2
Refinement stepCycle: final / Resolution: 1.43→19.093 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 48 223 3737
Biso mean--25.16 25.02 -
Num. residues----462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0233615
X-RAY DIFFRACTIONf_angle_d0.9594926
X-RAY DIFFRACTIONf_chiral_restr0.081560
X-RAY DIFFRACTIONf_plane_restr0.006644
X-RAY DIFFRACTIONf_dihedral_angle_d17.1111244
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.43-1.48110.52961460.5202701396
1.4811-1.54040.42561310.4241700097
1.5404-1.61040.39671440.3616706197
1.6104-1.69530.34131400.3298708997
1.6953-1.80140.38631510.3089709298
1.8014-1.94040.34661470.2801709797
1.9404-2.13540.29191480.269709197
2.1354-2.44390.30721460.2654712398
2.4439-3.0770.32841540.2557717398
3.077-19.0930.24671510.2054718397

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