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- PDB-8hxp: Crystal structure of B1 VIM-2 MBL in complex with 2-amino-5-(but-... -

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Basic information

Entry
Database: PDB / ID: 8hxp
TitleCrystal structure of B1 VIM-2 MBL in complex with 2-amino-5-(but-3-en-1-yl)thiazole-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 / 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-5YT / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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

Downloads & links

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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)50,0178
Polymers49,3592
Non-polymers6586
Water4,972276
1
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0084
Polymers24,6791
Non-polymers3293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-79 kcal/mol
Surface area9380 Å2
MethodPISA
2
B: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0084
Polymers24,6791
Non-polymers3293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.958, 90.202, 125.082
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 2
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.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-5YT / 2-azanyl-5-but-3-enyl-1,3-thiazole-4-carboxylic acid


Mass: 198.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10N2O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.63 Å3/Da / Density % sol: 53.17 %
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: Jul 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→19.84 Å / Num. obs: 38622 / % possible obs: 97.57 % / Redundancy: 12.7 % / CC1/2: 0.999 / Net I/σ(I): 13.8
Reflection shellResolution: 1.94→2.01 Å / Num. unique obs: 3317 / CC1/2: 0.795

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Processing

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

7dv0


Resolution: 1.94→19.753 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.81 / Phase error: 23.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 1996 5.59 %
Rwork0.1726 --
obs0.1752 35720 90.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.94→19.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 30 276 3772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153594
X-RAY DIFFRACTIONf_angle_d1.0524892
X-RAY DIFFRACTIONf_dihedral_angle_d14.7272080
X-RAY DIFFRACTIONf_chiral_restr0.058560
X-RAY DIFFRACTIONf_plane_restr0.007642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.98480.33681230.30962079X-RAY DIFFRACTION79
1.9848-2.03840.30111480.23892491X-RAY DIFFRACTION96
2.0384-2.09830.27281480.22032527X-RAY DIFFRACTION96
2.0983-2.16590.24321480.20962496X-RAY DIFFRACTION96
2.1659-2.24330.27391470.20342499X-RAY DIFFRACTION95
2.2433-2.33290.24271480.19462482X-RAY DIFFRACTION94
2.3329-2.43890.25091470.18282465X-RAY DIFFRACTION93
2.4389-2.56730.24591460.17682463X-RAY DIFFRACTION93
2.5673-2.72770.21221450.17642458X-RAY DIFFRACTION92
2.7277-2.93770.22861430.17272421X-RAY DIFFRACTION92
2.9377-3.23220.21851440.16892421X-RAY DIFFRACTION90
3.2322-3.69720.21551420.14872406X-RAY DIFFRACTION89
3.6972-4.64810.15841390.13982348X-RAY DIFFRACTION86
4.6481-19.7530.17351280.15382168X-RAY DIFFRACTION76

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