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- PDB-7du1: Crystal structure of VIM-2 MBL in complex with 1-propyl-1H-imidaz... -

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Basic information

Entry
Database: PDB / ID: 7du1
TitleCrystal structure of VIM-2 MBL in complex with 1-propyl-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


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-propylimidazole-2-carboxylic acid / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 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 7, 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
Water1,892105
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-78 kcal/mol
Surface area9500 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 area9520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.302, 79.580, 67.842
Angle α, β, γ (deg.)90.000, 130.910, 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
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-HKR / 1-propylimidazole-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.: 105 / 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: 42.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M 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: BL18U1 / 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: 1.79→50 Å / Num. obs: 38306 / % possible obs: 99.4 % / Redundancy: 5.9 % / Biso Wilson estimate: 18.67 Å2 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.067 / Rrim(I) all: 0.163 / Χ2: 0.885 / Net I/σ(I): 4.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.79-1.835.90.57318990.7560.2560.6290.52599.4
1.83-1.865.90.49319110.8250.2220.5410.5699.7
1.86-1.95.90.51218910.8270.230.5620.74599.4
1.9-1.945.90.55519380.750.2520.6111.03499.6
1.94-1.985.80.39518970.8620.1780.4340.77999.6
1.98-2.035.70.31718880.9090.1440.3490.78499.3
2.03-2.085.30.36318950.6910.170.4021.2498.5
2.08-2.136.10.29119070.9270.1290.3180.91999.5
2.13-2.260.24619160.9250.110.270.87399.6
2.2-2.275.90.28919280.8850.1330.3191.12799.6
2.27-2.355.90.22319080.9460.1020.2460.91799.8
2.35-2.445.70.19619230.9570.0910.2170.92299.5
2.44-2.555.60.18618840.9540.0870.2050.96298.7
2.55-2.696.10.17419290.9590.0790.1910.97299.8
2.69-2.866.10.15619290.9620.0710.1720.87999.7
2.86-3.0860.14219180.9680.0650.1570.84999.8
3.08-3.395.70.13519300.9680.0620.1490.90899.1
3.39-3.886.10.12619240.9720.0570.1390.84899.7
3.88-4.885.70.12319220.9750.0560.1360.9298.9
4.88-5060.12719690.9820.0580.140.97499.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.79 Å39.79 Å
Translation1.79 Å39.79 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.6.0phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LCA

5lca


Resolution: 1.79→39.79 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2596 2031 5.47 %
Rwork0.214 35090 -
obs0.2165 37121 94.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 55.83 Å2 / Biso mean: 20.1987 Å2 / Biso min: 8.03 Å2
Refinement stepCycle: final / Resolution: 1.79→39.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 40 105 3611
Biso mean--23.47 21.41 -
Num. residues----462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.023604
X-RAY DIFFRACTIONf_angle_d0.854890
X-RAY DIFFRACTIONf_chiral_restr0.054560
X-RAY DIFFRACTIONf_plane_restr0.005642
X-RAY DIFFRACTIONf_dihedral_angle_d12.3782078
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7902-1.83180.3255920.2317136556
1.8318-1.87760.29581230.2397222691
1.8776-1.92840.30851290.2773228193
1.9284-1.98510.30461390.2351237397
1.9851-2.04920.26641350.2192240298
2.0492-2.12240.27111430.2245238698
2.1224-2.20740.27351340.2183244699
2.2074-2.30790.30681420.2415244499
2.3079-2.42950.28421430.2222247599
2.4295-2.58170.26961360.2297240598
2.5817-2.7810.29061430.2248243299
2.781-3.06080.28241450.22472475100
3.0608-3.50350.20841370.205244999
3.5035-4.41310.22341420.1838246499
4.4131-39.790.23391480.1926246798

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