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- PDB-8y4i: Metal Beta-Lactamase VIM-2 in Complex with MBL inhibitor B7 -

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Basic information

Entry
Database: PDB / ID: 8y4i
TitleMetal Beta-Lactamase VIM-2 in Complex with MBL inhibitor B7
ComponentsMetal Beta-Lactamase VIM-2
KeywordsMETAL BINDING PROTEIN/INHIBITOR / METAL BINDING PROTEIN-INHIBITOR Complex
Function / homology: / FORMIC ACID
Function and homology information
Biological speciesEnterobacteriaceae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.935 Å
AuthorsLi, G.-B. / Wang, S.-Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Discovery of 2-((1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-3-yl)methyl)acrylic acids as potent MBL inhibitors
Authors: Liang, G.-Q. / Wang, S.-Y. / Li, G.-B.
History
DepositionJan 30, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metal Beta-Lactamase VIM-2
B: Metal Beta-Lactamase VIM-2
C: Metal Beta-Lactamase VIM-2
D: Metal Beta-Lactamase VIM-2
E: Metal Beta-Lactamase VIM-2
F: Metal Beta-Lactamase VIM-2
G: Metal Beta-Lactamase VIM-2
H: Metal Beta-Lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,39933
Polymers196,2828
Non-polymers3,11725
Water4,270237
1
A: Metal Beta-Lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9194
Polymers24,5351
Non-polymers3843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metal Beta-Lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9194
Polymers24,5351
Non-polymers3843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Metal Beta-Lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9655
Polymers24,5351
Non-polymers4304
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Metal Beta-Lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9194
Polymers24,5351
Non-polymers3843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Metal Beta-Lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9194
Polymers24,5351
Non-polymers3843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Metal Beta-Lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9194
Polymers24,5351
Non-polymers3843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Metal Beta-Lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9194
Polymers24,5351
Non-polymers3843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Metal Beta-Lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9194
Polymers24,5351
Non-polymers3843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.146, 245.800, 87.969
Angle α, β, γ (deg.)90.00, 93.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Metal Beta-Lactamase VIM-2


Mass: 24535.287 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteriaceae (bacteria) / Gene: blaVIM2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-A1LXF / 2-[[(9R)-2-fluoranyl-7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1,3,5-trien-9-yl]methyl]prop-2-enoic acid


Mass: 253.011 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H11BFO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.21 Å3/Da / Density % sol: 44.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 28% PEG3350,0.2M Magnesium formate

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Data collection

DiffractionMean temperature: 195 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Jun 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.93→122.9 Å / Num. obs: 123384 / % possible obs: 98 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 13.3
Reflection shellResolution: 1.93→122.9 Å / Num. unique obs: 3982 / CC1/2: 0.999

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Processing

Software
NameVersionClassification
PHENIX1.21-5207refinement
Aimlessdata scaling
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.935→43.89 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2437 1994 1.62 %
Rwork0.1913 --
obs0.1922 123244 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.935→43.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13864 0 163 237 14264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02614428
X-RAY DIFFRACTIONf_angle_d1.15619666
X-RAY DIFFRACTIONf_dihedral_angle_d17.1318408
X-RAY DIFFRACTIONf_chiral_restr0.0622248
X-RAY DIFFRACTIONf_plane_restr0.0082568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.935-1.98320.31231360.25458514X-RAY DIFFRACTION96
1.9832-2.03680.27381470.23298618X-RAY DIFFRACTION98
2.0368-2.09670.32071470.22668755X-RAY DIFFRACTION99
2.0967-2.16440.2731350.22368638X-RAY DIFFRACTION99
2.1644-2.24180.27191500.21468816X-RAY DIFFRACTION99
2.2418-2.33150.27251430.21358674X-RAY DIFFRACTION99
2.3315-2.43760.26671430.20718713X-RAY DIFFRACTION98
2.4376-2.56610.24351420.20168707X-RAY DIFFRACTION99
2.5661-2.72690.25991400.20628662X-RAY DIFFRACTION98
2.7269-2.93740.241430.19998677X-RAY DIFFRACTION98
2.9374-3.23290.26811380.28574X-RAY DIFFRACTION97
3.2329-3.70050.25031410.1788625X-RAY DIFFRACTION97
3.7005-4.66140.20531450.15658558X-RAY DIFFRACTION97
4.6614-43.890.19021440.16298719X-RAY DIFFRACTION98

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