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- PDB-7dv1: Crystal structure of VIM-2 MBL in complex with 1-(4-hydroxybenzyl... -

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Basic information

Entry
Database: PDB / ID: 7dv1
TitleCrystal structure of VIM-2 MBL in complex with 1-(4-hydroxybenzyl)-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 / Chem-HN9 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.966 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 Natural Science Foundation of China (NSFC)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 12, 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)50,37214
Polymers49,3592
Non-polymers1,01312
Water4,216234
1
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1867
Polymers24,6791
Non-polymers5066
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-108 kcal/mol
Surface area9490 Å2
MethodPISA
2
B: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1867
Polymers24,6791
Non-polymers5066
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-106 kcal/mol
Surface area9390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.946, 79.457, 68.040
Angle α, β, γ (deg.)90.000, 130.560, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-440-

HOH

21B-411-

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-HN9 / 1-[(4-hydroxyphenyl)methyl]imidazole-2-carboxylic acid


Mass: 218.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H10N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


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


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.12 Å3/Da / Density % sol: 42 %
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: Dec 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.966→50 Å / Num. obs: 29247 / % possible obs: 99.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 21.59 Å2 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.048 / Rrim(I) all: 0.126 / Χ2: 0.959 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.97-26.10.32513250.930.140.3550.94290.8
2-2.046.90.30314510.9430.1250.3280.981100
2.04-2.086.90.27114550.9570.1110.2931.008100
2.08-2.126.90.25514640.9610.1040.2761.01499.9
2.12-2.176.80.23314850.9650.0960.2521100
2.17-2.226.80.22214650.970.0910.241.01399.9
2.22-2.276.50.2114690.9660.0880.2291.051100
2.27-2.346.30.18814590.9720.080.2051.068100
2.34-2.470.18114590.9740.0730.1961.105100
2.4-2.4870.16314670.9720.0670.1760.996100
2.48-2.5770.15414610.980.0630.1661.00599.9
2.57-2.676.80.1414670.9780.0590.1520.9699.9
2.67-2.86.50.1314540.980.0550.1410.94199.8
2.8-2.946.80.12114860.9870.050.1310.92299.9
2.94-3.137.10.11414680.9870.0460.1230.886100
3.13-3.3770.10814790.9840.0450.1170.89100
3.37-3.716.50.10514660.9860.0440.1140.83999.1
3.71-4.247.20.114670.9830.040.1080.8299.9
4.24-5.356.80.114920.9910.0410.1080.85599.8
5.35-506.80.115080.9880.0420.1090.89699.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.97 Å39.73 Å
Translation1.97 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: 5LCA

5lca


Resolution: 1.966→39.728 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2356 2007 6.88 %
Rwork0.181 27154 -
obs0.1847 29161 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.68 Å2 / Biso mean: 21.778 Å2 / Biso min: 9.38 Å2
Refinement stepCycle: final / Resolution: 1.966→39.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 50 235 3751
Biso mean--24.1 25.9 -
Num. residues----462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0213617
X-RAY DIFFRACTIONf_angle_d0.8284908
X-RAY DIFFRACTIONf_chiral_restr0.056560
X-RAY DIFFRACTIONf_plane_restr0.005644
X-RAY DIFFRACTIONf_dihedral_angle_d13.6762078
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.966-2.01470.281280.195178491
2.0147-2.06920.27641490.18761923100
2.0692-2.13010.25621460.1871969100
2.1301-2.19880.26861450.18011927100
2.1988-2.27740.23081320.1911951100
2.2774-2.36860.24911420.18971947100
2.3686-2.47640.25591400.19361951100
2.4764-2.60690.22831430.19681959100
2.6069-2.77020.2841510.20331944100
2.7702-2.9840.29461470.20371961100
2.984-3.28420.2891480.18951942100
3.2842-3.75910.20821430.1811194299
3.7591-4.73480.19061450.15131967100
4.7348-39.7280.18131480.1636198799

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