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- PDB-6tgi: Crystal structure of VIM-2 in complex with triazole-based inhibit... -

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Basic information

Entry
Database: PDB / ID: 6tgi
TitleCrystal structure of VIM-2 in complex with triazole-based inhibitor OP24
ComponentsVim-1
KeywordsHYDROLASE / New Delhi metallo-beta-lactamase
Function / homology
Function and homology information


membrane => GO:0016020 / antibiotic catabolic process / beta-lactamase activity / 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-N8Z / Vim-1 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMaso, L. / Spirakis, F. / Santucci, M. / Simon, C. / Docquier, J.D. / Cruciani, G. / Costi, M.P. / Tondi, D. / Cendron, L.
Funding support Italy, 1items
OrganizationGrant numberCountry
European Communitys Seventh Framework Programme286998 Italy
CitationJournal: Sci Rep / Year: 2020
Title: Virtual screening identifies broad-spectrum beta-lactamase inhibitors with activity on clinically relevant serine- and metallo-carbapenemases.
Authors: Spyrakis, F. / Santucci, M. / Maso, L. / Cross, S. / Gianquinto, E. / Sannio, F. / Verdirosa, F. / De Luca, F. / Docquier, J.D. / Cendron, L. / Tondi, D. / Venturelli, A. / Cruciani, G. / Costi, M.P.
History
DepositionNov 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vim-1
B: Vim-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,56018
Polymers52,2842
Non-polymers1,27616
Water9,134507
1
A: Vim-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7809
Polymers26,1421
Non-polymers6388
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-37 kcal/mol
Surface area10100 Å2
MethodPISA
2
B: Vim-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7809
Polymers26,1421
Non-polymers6388
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-38 kcal/mol
Surface area9870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.618, 79.060, 68.207
Angle α, β, γ (deg.)90.000, 131.170, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Vim-1


Mass: 26142.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Missing residues are present in the crystallized protein but not visible in the electron density maps.
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blm, NCTC13437_04762 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A485HTJ5, UniProt: Q9K2N0*PLUS, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-N8Z / 5-(4-chloranyl-1,5-dimethyl-pyrazol-3-yl)-4-ethyl-1,2,4-triazole-3-thiol


Mass: 257.743 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12ClN5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 507 / 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: 2.01 Å3/Da / Density % sol: 38.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.25 M Magnesium Formate, 27 % PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.001 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.001 Å / Relative weight: 1
ReflectionResolution: 1.6→39.56 Å / Num. obs: 54492 / % possible obs: 97.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.2
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5436

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZ3

4bz3


Resolution: 1.6→39.56 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.101 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2726 5 %RANDOM
Rwork0.178 ---
obs0.18 51766 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 72.09 Å2 / Biso mean: 21.35 Å2 / Biso min: 9.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20.1 Å2
2---0.04 Å20 Å2
3----0.18 Å2
Refinement stepCycle: final / Resolution: 1.6→39.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3477 0 62 507 4046
Biso mean--25.69 31.4 -
Num. residues----464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123698
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7191.6435062
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7175480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89422.022183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96615533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2821524
X-RAY DIFFRACTIONr_chiral_restr0.1670.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022912
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 217 -
Rwork0.24 3795 -
all-4012 -
obs--99.7 %

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