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- PDB-7dyy: Crystal structure of VIM-2 MBL in complex with 1-((2-aminobenzo[d... -

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Basic information

Entry
Database: PDB / ID: 7dyy
TitleCrystal structure of VIM-2 MBL in complex with 1-((2-aminobenzo[d]thiazol-6-yl)methyl)-1H-imidazole-2-carboxylic acid
ComponentsBeta-lactamase class B VIM-2
KeywordsHYDROLASE / Metallo-beta-lactamase VIM-2 / VIM-2
Function / homology
Function and homology information


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-HQF / DI(HYDROXYETHYL)ETHER / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 Å
AuthorsYan, Y.-H. / Li, G.-B.
Funding support China, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)81874291 China
National Science Foundation (NSF, China)81502989 China
National Science Foundation (NSF, China)82073698 China
CitationJournal: Eur.J.Med.Chem. / Year: 2022
Title: Structure-guided optimization of 1H-imidazole-2-carboxylic acid derivatives affording potent VIM-Type metallo-beta-lactamase inhibitors.
Authors: Yan, Y.H. / Li, W. / Chen, W. / Li, C. / Zhu, K.R. / Deng, J. / Dai, Q.Q. / Yang, L.L. / Wang, Z. / Li, G.B.
History
DepositionJan 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 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

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)50,38110
Polymers49,3592
Non-polymers1,0228
Water2,324129
1
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1915
Polymers24,6791
Non-polymers5114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-28 kcal/mol
Surface area9510 Å2
MethodPISA
2
B: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1915
Polymers24,6791
Non-polymers5114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-66 kcal/mol
Surface area9570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.123, 45.080, 98.028
Angle α, β, γ (deg.)90.000, 90.060, 90.000
Int Tables number4
Space group name H-MP1211

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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 / 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-HQF / 1-[(2-azanyl-1,3-benzothiazol-6-yl)methyl]imidazole-2-carboxylic acid


Mass: 274.298 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H10N4O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.74 Å3/Da / Density % sol: 55.05 %
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: Oct 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.798→98.03 Å / Num. obs: 26848 / % possible obs: 99.7 % / Redundancy: 6 % / Biso Wilson estimate: 23.35 Å2 / CC1/2: 0.919 / Rmerge(I) obs: 0.482 / Rpim(I) all: 0.221 / Rrim(I) all: 0.532 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.798-2.946.51.1781276419700.6930.5081.2854.5100
2.94-98.034.60.08220884570.9890.0430.09311.797.1

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LCA

5lca


Resolution: 1.798→51.841 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 40.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2981 1978 7.37 %
Rwork0.2316 24870 -
obs0.2366 26848 53.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.34 Å2 / Biso mean: 29.013 Å2 / Biso min: 10.3 Å2
Refinement stepCycle: final / Resolution: 1.798→51.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 56 129 3651
Biso mean--34.15 27.01 -
Num. residues----462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183621
X-RAY DIFFRACTIONf_angle_d1.3714928
X-RAY DIFFRACTIONf_chiral_restr0.064560
X-RAY DIFFRACTIONf_plane_restr0.008644
X-RAY DIFFRACTIONf_dihedral_angle_d15.6992084
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7983-1.84320.502130.2677491
1.8432-1.89310.2916190.30472337
1.8931-1.94880.4531400.270450115
1.9488-2.01170.2971620.275576523
2.0117-2.08360.3199920.2617112634
2.0836-2.1670.36681200.2767150346
2.167-2.26570.31641360.2953170552
2.2657-2.38510.34221580.2873193159
2.3851-2.53450.34191790.3047219266
2.5345-2.73020.37321890.295242574
2.7302-3.00490.34072110.281272282
3.0049-3.43970.30932390.2401299490
3.4397-4.33330.2842630.1874330599
4.3333-51.8410.23072670.1844341999

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