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- PDB-9f0s: VIM-2 in complex with GKV63 (5j) - dynamically chiral phosphonic ... -

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Basic information

Entry
Database: PDB / ID: 9f0s
TitleVIM-2 in complex with GKV63 (5j) - 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


beta-lactamase / 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 / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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

Downloads & links

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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)55,93414
Polymers54,7032
Non-polymers1,23112
Water11,187621
1
A: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9677
Polymers27,3511
Non-polymers6166
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9677
Polymers27,3511
Non-polymers6166
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.506, 79.244, 67.716
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-554-

HOH

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Components

#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
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-A1H8U / [(~{R})-(2-hydroxyphenyl)-(2-thiophen-3-ylethanoylamino)methyl]phosphonic acid


Mass: 327.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H14NO5PS / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H2O
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: 1.9 Å3/Da / Density % sol: 35.14 %
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: 1.11→55.4 Å / Num. obs: 100869 / % possible obs: 79.2 % / Redundancy: 6.7 % / Biso Wilson estimate: 13.24 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.02 / Rrim(I) all: 0.054 / Net I/σ(I): 16.2
Reflection shellResolution: 1.11→1.22 Å / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5044 / CC1/2: 0.742 / Rpim(I) all: 0.471 / Rrim(I) all: 0.774

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.20.1_4487refinement
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→55.34 Å / SU ML: 0.142 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.2364
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.186 3842 4.96 %
Rwork0.1716 73690 -
obs0.1724 77532 96.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.33 Å2
Refinement stepCycle: LAST / Resolution: 1.4→55.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 60 621 4167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00663801
X-RAY DIFFRACTIONf_angle_d0.96645240
X-RAY DIFFRACTIONf_chiral_restr0.0859596
X-RAY DIFFRACTIONf_plane_restr0.0086692
X-RAY DIFFRACTIONf_dihedral_angle_d11.501564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.25981320.23382401X-RAY DIFFRACTION85.06
1.42-1.440.28111220.24522543X-RAY DIFFRACTION90.25
1.44-1.460.27411250.2282660X-RAY DIFFRACTION93.43
1.46-1.480.25541340.22022653X-RAY DIFFRACTION95.91
1.48-1.50.23071750.21742705X-RAY DIFFRACTION97.13
1.5-1.520.2351660.21462731X-RAY DIFFRACTION97.35
1.52-1.550.28171720.21292684X-RAY DIFFRACTION96.88
1.55-1.570.24031280.20852756X-RAY DIFFRACTION96.91
1.57-1.60.24241370.20262762X-RAY DIFFRACTION97.45
1.6-1.630.24261240.20342744X-RAY DIFFRACTION97.45
1.63-1.670.21071600.19562714X-RAY DIFFRACTION97.32
1.67-1.70.22891650.19182728X-RAY DIFFRACTION97.11
1.7-1.740.22851400.17992751X-RAY DIFFRACTION97.8
1.74-1.790.21981000.19152790X-RAY DIFFRACTION97.4
1.79-1.830.20721020.18392789X-RAY DIFFRACTION97.9
1.83-1.890.22481600.18252767X-RAY DIFFRACTION97.79
1.89-1.950.19811540.17732753X-RAY DIFFRACTION98.48
1.95-2.020.20621480.16622771X-RAY DIFFRACTION98.28
2.02-2.10.16281400.16382770X-RAY DIFFRACTION97.95
2.1-2.20.19251320.16942765X-RAY DIFFRACTION97.74
2.2-2.310.18981210.16962811X-RAY DIFFRACTION98.29
2.31-2.460.18481000.16652791X-RAY DIFFRACTION97.27
2.46-2.650.16611270.17072757X-RAY DIFFRACTION96.84
2.65-2.910.1861280.17092849X-RAY DIFFRACTION99.17
2.91-3.330.15581840.15382759X-RAY DIFFRACTION98.73
3.33-4.20.13411760.13912761X-RAY DIFFRACTION97.93
4.2-55.340.17271900.15372725X-RAY DIFFRACTION95.29

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