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- PDB-7dub: Crystal structure of VIM-2 MBL in complex with 1-isopropyl-1H-imi... -

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Basic information

Entry
Database: PDB / ID: 7dub
TitleCrystal structure of VIM-2 MBL in complex with 1-isopropyl-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
FORMIC ACID / 1-propan-2-ylimidazole-2-carboxylic acid / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.599 Å
AuthorsLi, G.-B. / Yan, Y.-H.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81874291 China
National Natural Science Foundation of China (NSFC)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 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 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)50,24414
Polymers49,3592
Non-polymers88512
Water10,305572
1
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1227
Polymers24,6791
Non-polymers4426
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-79 kcal/mol
Surface area9550 Å2
MethodPISA
2
B: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1227
Polymers24,6791
Non-polymers4426
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-80 kcal/mol
Surface area9470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.909, 79.454, 67.394
Angle α, β, γ (deg.)90.000, 129.900, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-460-

HOH

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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.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HKU / 1-propan-2-ylimidazole-2-carboxylic acid


Mass: 154.166 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / 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: 2.1 Å3/Da / Density % sol: 41.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Magnesium Formate, 21%-27% (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 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.599→50 Å / Num. obs: 53434 / % possible obs: 99.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 11.63 Å2 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.044 / Rrim(I) all: 0.118 / Χ2: 0.955 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.636.90.26526400.9580.1070.2860.963100
1.63-1.6670.25126830.9520.1020.2710.98399.9
1.66-1.696.90.23226900.9580.0940.2511.00599.9
1.69-1.726.90.2126670.9660.0850.2271.01699.8
1.72-1.766.70.19426650.9680.080.2110.97999.6
1.76-1.86.40.18326520.970.0770.1991.01399.4
1.8-1.856.80.17326560.9720.0710.1871.08799.5
1.85-1.97.10.16226750.9790.0650.1741.07199.9
1.9-1.9570.15526580.9730.0630.1681.04699.6
1.95-2.0270.14626810.9780.0590.1581.04399.7
2.02-2.096.90.13626710.9810.0550.1471.01899.4
2.09-2.176.50.13126410.9830.0550.1420.98798.7
2.17-2.2770.12626940.9830.0510.1360.95599.5
2.27-2.397.10.12126610.9780.0480.130.9399.7
2.39-2.547.10.11826850.980.0470.1270.90299.8
2.54-2.746.90.11226650.9840.0450.1210.88298.9
2.74-3.016.90.1126530.9850.0450.1190.89898.6
3.01-3.457.20.10526930.9890.0420.1130.86899.9
3.45-4.346.80.09826830.9860.040.1060.79798.5
4.34-507.10.0927210.9910.0360.0970.67898.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.24 Å39.73 Å
Translation6.24 Å39.73 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.6.0phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JN6

6jn6


Resolution: 1.599→39.727 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1999 2000 3.75 %
Rwork0.1645 51376 -
obs0.1659 53376 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 45.07 Å2 / Biso mean: 14.422 Å2 / Biso min: 4.28 Å2
Refinement stepCycle: final / Resolution: 1.599→39.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 40 575 4081
Biso mean--18.98 23.04 -
Num. residues----462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0193609
X-RAY DIFFRACTIONf_angle_d0.8274892
X-RAY DIFFRACTIONf_chiral_restr0.054560
X-RAY DIFFRACTIONf_plane_restr0.005642
X-RAY DIFFRACTIONf_dihedral_angle_d15.6242076
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.599-1.6390.2391290.184353696
1.639-1.68330.23021580.18163726100
1.6833-1.73280.21761340.1711363799
1.7328-1.78880.18751410.17273636100
1.7888-1.85270.20351470.1767364999
1.8527-1.92690.23911390.17513710100
1.9269-2.01460.21141480.16913668100
2.0146-2.12080.21531460.1594367999
2.1208-2.25360.19161400.1625366199
2.2536-2.42760.20331470.16843705100
2.4276-2.67190.21941440.1734367799
2.6719-3.05840.20131360.1796367699
3.0584-3.85270.1811440.15133711100
3.8527-39.7270.17391470.1462370598

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