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- PDB-9f0q: VIM-2 in complex with GKV53 (5d) - dynamically chiral phosphonic ... -

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Basic information

Entry
Database: PDB / ID: 9f0q
TitleVIM-2 in complex with GKV53 (5d) - dynamically chiral phosphonic acid-type metallo-beta-lactamase inhibitors
ComponentsMetallo-beta-lactamase type 2
KeywordsANTIBIOTIC / beta-lactamase / metallo-beta-lactamase / inhibitor
Function / homology
Function and homology information


: / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
: / : / FORMIC ACID / Metallo-beta-lactamase VIM-2-like protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsBartels, K. / Prester, A. / Bosman, R. / Gulyas, K.V. / Erdelyi, M. / Schulz, E.C.
Funding support Germany, Sweden, 5items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research01KI2114 Germany
German Research Foundation (DFG)458246365 Germany
Max Planck Society Germany
Swedish Research Council2013-8804 Sweden
Uppsala Antibiotic Center Sweden
CitationJournal: Commun Chem / Year: 2025
Title: Dynamically chiral phosphonic acid-type metallo-beta-lactamase inhibitors.
Authors: Gulyas, K.V. / Zhou, L. / Salamonsen, D. / Prester, A. / Bartels, K. / Bosman, R. / Haffke, P. / Li, J. / Tamasi, V. / Deufel, F. / Thoma, J. / Andersson Rasmussen, A. / Csala, M. / Schroder ...Authors: Gulyas, K.V. / Zhou, L. / Salamonsen, D. / Prester, A. / Bartels, K. / Bosman, R. / Haffke, P. / Li, J. / Tamasi, V. / Deufel, F. / Thoma, J. / Andersson Rasmussen, A. / Csala, M. / Schroder Leiros, H.K. / Xu, Z. / Widersten, M. / Rohde, H. / Schulz, E.C. / Zhu, W. / Erdelyi, M.
History
DepositionApr 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metallo-beta-lactamase type 2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,36915
Polymers54,7032
Non-polymers1,66713
Water8,395466
1
A: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0037
Polymers27,3511
Non-polymers6526
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3668
Polymers27,3511
Non-polymers1,0157
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.804, 79.021, 67.815
Angle α, β, γ (deg.)90.000, 130.760, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-453-

HOH

21B-524-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Metallo-beta-lactamase type 2 / B2 metallo-beta-lactamase / Metallo-beta-lactamase type II


Mass: 27351.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The gene sequence coding for residues Val25 to Glu300 of VIM-2 was isolated from Pseudomonas aeruginosa strain 301 5473. Protein was purified as a construct with His6-tag (residues 1-7) and ...Details: The gene sequence coding for residues Val25 to Glu300 of VIM-2 was isolated from Pseudomonas aeruginosa strain 301 5473. Protein was purified as a construct with His6-tag (residues 1-7) and TEV protease cleavage site (residues 8-14).
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: 301-5473 / Gene: blaVIM / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B8QIQ9, beta-lactamase

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Non-polymers , 5 types, 479 molecules

#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-A1IJ9 / [(S)-(1-benzothiophen-3-ylcarbonylamino)-(2-hydroxyphenyl)methyl]phosphonic acid / ((Benzo[b]thiophene-3-carboxamido)(2-hydroxyphenyl)methyl)phosphonic acid


Mass: 363.325 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H14NO5PS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Zn
#5: Chemical ChemComp-A1H8W / [(R)-(1-benzothiophen-3-ylcarbonylamino)-(2-hydroxyphenyl)methyl]phosphonic acid / ((Benzo[b]thiophene-3-carboxamido)(2-hydroxyphenyl)methyl)phosphonic acid


Mass: 363.325 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14NO5PS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 1.89 Å3/Da / Density % sol: 34.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: protein solution: 10.3 mg/ml in 50 mM Tris/HCl, pH 7.2, 100 uM ZnCl2 crystallization agent: 20 mM inhibitor, 25% polyethylene glycol (PEG) 3350, 0.2 M magnesium formate cryo protectant ...Details: protein solution: 10.3 mg/ml in 50 mM Tris/HCl, pH 7.2, 100 uM ZnCl2 crystallization agent: 20 mM inhibitor, 25% polyethylene glycol (PEG) 3350, 0.2 M magnesium formate cryo protectant solution: (20 mM inhibitor, 25% PEG3350, 15% Ethylene glycol, 0.2 mM MgCl2, 50 mM HEPES pH 7.2)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.8 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.92→55.19 Å / Num. obs: 30937 / % possible obs: 99.3 % / Redundancy: 7 % / Biso Wilson estimate: 21.69 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.058 / Rrim(I) all: 0.154 / Net I/σ(I): 9.8
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1551 / CC1/2: 0.802 / Rpim(I) all: 0.397 / Rrim(I) all: 1.066 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
autoPROC1.1.7data processing
autoPROC1.1.7data reduction
autoPROC1.1.7data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→55.19 Å / SU ML: 0.1778 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.2255
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2133 1535 4.97 %
Rwork0.1712 29372 -
obs0.1734 30907 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26 Å2
Refinement stepCycle: LAST / Resolution: 1.92→55.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 90 466 4042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073723
X-RAY DIFFRACTIONf_angle_d0.88935111
X-RAY DIFFRACTIONf_chiral_restr0.057575
X-RAY DIFFRACTIONf_plane_restr0.008669
X-RAY DIFFRACTIONf_dihedral_angle_d15.85921308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.980.26271400.22772662X-RAY DIFFRACTION99.15
1.98-2.050.26661460.19972646X-RAY DIFFRACTION99.29
2.05-2.130.25091130.18862660X-RAY DIFFRACTION99.04
2.14-2.230.25231740.18942619X-RAY DIFFRACTION98.83
2.23-2.350.22811450.18532683X-RAY DIFFRACTION99.68
2.35-2.50.28441100.17642693X-RAY DIFFRACTION99.54
2.5-2.690.24481290.17582674X-RAY DIFFRACTION99.26
2.69-2.960.21821240.1772698X-RAY DIFFRACTION99.37
2.96-3.390.21241280.16322674X-RAY DIFFRACTION98.98
3.39-4.270.17811760.14522650X-RAY DIFFRACTION99.54
4.27-55.190.17931500.16362713X-RAY DIFFRACTION98.93

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