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- PDB-9f0r: VIM-2 in complex with GKV65 (5g) - dynamically chiral phosphonic ... -

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Basic information

Entry
Database: PDB / ID: 9f0r
TitleVIM-2 in complex with GKV65 (5g) - 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: 1.3 Å
AuthorsBosman, R. / Prester, A. / Bartels, K. / 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)56,03815
Polymers54,7032
Non-polymers1,33613
Water11,980665
1
A: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0318
Polymers27,3511
Non-polymers6807
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0077
Polymers27,3511
Non-polymers6566
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.242, 79.146, 67.686
Angle α, β, γ (deg.)90.000, 130.380, 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
11B-550-

HOH

21B-682-

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, 678 molecules

#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-A1H8V / [(~{R})-(2-hydroxyphenyl)-(4,5,6,7-tetrahydro-2-benzothiophen-1-ylcarbonylamino)methyl]phosphonic acid


Mass: 367.357 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H18NO5PS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 665 / 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: 34.89 %
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: 1.05→55.24 Å / Num. obs: 115821 / % possible obs: 78.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 10.91 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.036 / Rrim(I) all: 0.068 / Net I/σ(I): 13.6
Reflection shellResolution: 1.05→1.15 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.902 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5792 / CC1/2: 0.62 / Rpim(I) all: 0.651 / Rrim(I) all: 0.992 / % possible all: 42.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
Cootmodel building
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→31.39 Å / SU ML: 0.1136 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.7123
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1691 4933 5.01 %
Rwork0.1365 93603 -
obs0.138 98536 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.26 Å2
Refinement stepCycle: LAST / Resolution: 1.3→31.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 67 665 4218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01433818
X-RAY DIFFRACTIONf_angle_d1.39885272
X-RAY DIFFRACTIONf_chiral_restr0.1045597
X-RAY DIFFRACTIONf_plane_restr0.0136697
X-RAY DIFFRACTIONf_dihedral_angle_d13.0507575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.21441570.18063096X-RAY DIFFRACTION98.52
1.31-1.330.21531580.17023091X-RAY DIFFRACTION98.37
1.33-1.350.22541520.15313071X-RAY DIFFRACTION97.79
1.35-1.360.19541560.13553111X-RAY DIFFRACTION97.84
1.36-1.380.17621480.13323098X-RAY DIFFRACTION98.39
1.38-1.40.18971440.12623115X-RAY DIFFRACTION98.25
1.4-1.420.18181860.12923066X-RAY DIFFRACTION98.4
1.42-1.440.19061850.13043070X-RAY DIFFRACTION98.43
1.44-1.460.17431930.12223060X-RAY DIFFRACTION98.34
1.46-1.490.18231410.12233125X-RAY DIFFRACTION98.14
1.49-1.510.1991560.1243079X-RAY DIFFRACTION98.36
1.51-1.540.17661430.11893112X-RAY DIFFRACTION97.92
1.54-1.570.17571480.12173123X-RAY DIFFRACTION98.52
1.57-1.60.1672000.11843092X-RAY DIFFRACTION99.04
1.6-1.640.1661780.1223117X-RAY DIFFRACTION99.22
1.64-1.680.18351890.12163113X-RAY DIFFRACTION99.43
1.68-1.720.17142010.12353079X-RAY DIFFRACTION99.42
1.72-1.760.17421700.12073127X-RAY DIFFRACTION99.37
1.76-1.820.17771670.12243134X-RAY DIFFRACTION99.61
1.82-1.870.1651860.11993141X-RAY DIFFRACTION99.64
1.87-1.940.15731950.12373106X-RAY DIFFRACTION99.61
1.94-2.020.17631420.11913124X-RAY DIFFRACTION99.06
2.02-2.110.1571290.11853192X-RAY DIFFRACTION98.96
2.11-2.220.17091550.12653113X-RAY DIFFRACTION98.79
2.22-2.360.16291140.14153169X-RAY DIFFRACTION98.74
2.36-2.540.16671650.14033182X-RAY DIFFRACTION99.88
2.54-2.80.17381910.1533149X-RAY DIFFRACTION99.88
2.8-3.20.17361570.15273175X-RAY DIFFRACTION99.73
3.21-4.040.14831680.13843167X-RAY DIFFRACTION99.2
4.04-31.390.16111590.15383206X-RAY DIFFRACTION98.83

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