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- PDB-7dz1: Crystal structure of VIM-2 MBL in complex with 1-benzyl-5-methyl-... -

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Basic information

Entry
Database: PDB / ID: 7dz1
TitleCrystal structure of VIM-2 MBL in complex with 1-benzyl-5-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


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-HQ3 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.708 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

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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)50,0538
Polymers49,3592
Non-polymers6946
Water41423
1
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0264
Polymers24,6791
Non-polymers3473
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)25,0264
Polymers24,6791
Non-polymers3473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.016, 79.112, 67.763
Angle α, β, γ (deg.)90.000, 130.530, 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 / 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-HQ3 / 5-methyl-1-(phenylmethyl)imidazole-2-carboxylic acid


Mass: 216.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.13 Å3/Da / Density % sol: 42.15 %
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: Jul 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.708→55.65 Å / Num. obs: 11329 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.946 / Rmerge(I) obs: 0.424 / Rpim(I) all: 0.176 / Rrim(I) all: 0.46 / Net I/σ(I): 5.4
Reflection shellResolution: 2.708→2.755 Å / Rmerge(I) obs: 1.153 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 541 / CC1/2: 0.643 / Rpim(I) all: 0.47 / Rrim(I) all: 1.246

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Processing

Software
NameVersionClassification
DENZOdata reduction
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
Aimlessdata scaling
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LCA

5lca


Resolution: 2.708→55.65 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.261 1139 10.06 %
Rwork0.1721 10187 -
obs0.1812 11326 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.99 Å2 / Biso mean: 12.3819 Å2 / Biso min: 0.16 Å2
Refinement stepCycle: final / Resolution: 2.708→55.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 36 23 3525
Biso mean--14.36 13.96 -
Num. residues----462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0573601
X-RAY DIFFRACTIONf_angle_d1.1614904
X-RAY DIFFRACTIONf_chiral_restr0.07560
X-RAY DIFFRACTIONf_plane_restr0.008644
X-RAY DIFFRACTIONf_dihedral_angle_d17.7382078
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7083-2.83160.36821420.20241262100
2.8316-2.98080.28271420.20521253100
2.9808-3.16760.29461350.18991263100
3.1676-3.41210.27741420.17421291100
3.4121-3.75540.27841410.16431264100
3.7554-4.29870.23051490.15121275100
4.2987-5.41520.2261450.14111276100
5.4152-55.650.21761430.1908130399

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