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- PDB-8hy2: Crystal structure of B1 VIM-2 MBL in complex with 2-amino-5-phene... -

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Basic information

Entry
Database: PDB / ID: 8hy2
TitleCrystal structure of B1 VIM-2 MBL in complex with 2-amino-5-phenethylthiazole-4-carboxylic acid
ComponentsBeta-lactamase class B VIM-2
KeywordsHYDROLASE / Beta-lactamase class B VIM-2
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / hydrolase activity / 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-5ZX / FORMIC ACID / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYan, Y.-H. / Zhu, K.-R. / Li, G.-B.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81874291 China
National Natural Science Foundation of China (NSFC)82122065 China
National Natural Science Foundation of China (NSFC)82073698 China
CitationJournal: J.Med.Chem. / Year: 2023
Title: Discovery of 2-Aminothiazole-4-carboxylic Acids as Broad-Spectrum Metallo-beta-lactamase Inhibitors by Mimicking Carbapenem Hydrolysate Binding.
Authors: Yan, Y.H. / Zhang, T.T. / Li, R. / Wang, S.Y. / Wei, L.L. / Wang, X.Y. / Zhu, K.R. / Li, S.R. / Liang, G.Q. / Yang, Z.B. / Yang, L.L. / Qin, S. / Li, G.B.
History
DepositionJan 5, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,1977
Polymers24,6791
Non-polymers5176
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-73 kcal/mol
Surface area9440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.248, 64.446, 91.034
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-427-

HOH

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Components

#1: Protein Beta-lactamase class B VIM-2 / BlaVIM-2 / Metallo-beta-lactamase / Metallo-beta-lactamase VIM-2 / VIM-2 beta-lactamase / VIM-2 ...BlaVIM-2 / Metallo-beta-lactamase / Metallo-beta-lactamase 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
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K2N0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-5ZX / 2-azanyl-5-(2-phenylethyl)-1,3-thiazole-4-carboxylic acid


Mass: 248.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12N2O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.75 Å3/Da / Density % sol: 55.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Magnesium Formate, 28%-35% (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: Nov 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 18859 / % possible obs: 98.9 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.147 / Χ2: 0.048 / Net I/σ(I): 5.1 / Num. measured all: 172141
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2-2.036.30.6438490.968191.6
2.03-2.077.10.6588971.015195.9
2.07-2.117.50.578911.018198
2.11-2.1580.6079391.063198.4
2.15-2.28.40.5179461.029199.5
2.2-2.258.50.4899031.029198.6
2.25-2.318.50.4689401.057199.2
2.31-2.379.10.439301.099199.6
2.37-2.449.90.3689291.052199.7
2.44-2.5210.10.3479331.063199.7
2.52-2.6110.10.3079501.047199.6
2.61-2.71100.269371.062199.8
2.71-2.849.70.229571.073199.9
2.84-2.99100.1929301.076199.8
2.99-3.1710.30.1539731.026199.7
3.17-3.4210.10.1299590.991100
3.42-3.769.60.1059680.9091100
3.76-4.3110.10.0969740.9141100
4.31-5.439.60.0889870.8581100
5.43-5090.10110670.957199.6

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data reduction
PHASERphasing
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DV0

7dv0


Resolution: 2→25.389 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2059 1818 10 %
Rwork0.1531 --
obs0.1584 18180 95.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→25.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1733 0 28 196 1957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181808
X-RAY DIFFRACTIONf_angle_d1.0212456
X-RAY DIFFRACTIONf_dihedral_angle_d13.2871040
X-RAY DIFFRACTIONf_chiral_restr0.058280
X-RAY DIFFRACTIONf_plane_restr0.006322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05360.26341010.187911X-RAY DIFFRACTION72
2.0536-2.1140.24491270.18061134X-RAY DIFFRACTION87
2.114-2.18220.22661340.17691213X-RAY DIFFRACTION94
2.1822-2.26020.23931390.16671243X-RAY DIFFRACTION96
2.2602-2.35060.21821400.16271269X-RAY DIFFRACTION98
2.3506-2.45750.20741450.1561305X-RAY DIFFRACTION100
2.4575-2.5870.26971450.14941301X-RAY DIFFRACTION100
2.587-2.74890.20261440.15411301X-RAY DIFFRACTION100
2.7489-2.96080.18091460.16041310X-RAY DIFFRACTION100
2.9608-3.25820.22471460.14731323X-RAY DIFFRACTION100
3.2582-3.72840.18191480.14481322X-RAY DIFFRACTION100
3.7284-4.69260.16241500.13071356X-RAY DIFFRACTION99
4.6926-25.3890.21521530.161374X-RAY DIFFRACTION97

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