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- PDB-8pg3: Crystal structure of the metallo-beta-lactamase VIM1 with 2729 -

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Basic information

Entry
Database: PDB / ID: 8pg3
TitleCrystal structure of the metallo-beta-lactamase VIM1 with 2729
ComponentsBeta-lactamase VIM-1
KeywordsANTIMICROBIAL PROTEIN / Complex / metallo-beta-lactamase / inhibitor / zinc / indole carboxylate
Function / homology: / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / metal ion binding / : / Beta-lactamase VIM-1
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsCalvopina, K. / Brem, J. / Farley, A.J.M. / Allen, M.D. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust099141/Z/12/Z United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of the metallo-beta-lactamase VIM1 with 2729
Authors: Calvopina, K. / Brem, J. / Farley, A.J.M. / Allen, M.D. / Schofield, C.J.
History
DepositionJun 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase VIM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6864
Polymers28,0511
Non-polymers6343
Water6,269348
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-79 kcal/mol
Surface area9250 Å2
Unit cell
Length a, b, c (Å)39.520, 67.960, 40.340
Angle α, β, γ (deg.)90.000, 93.780, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Beta-lactamase VIM-1 / Class B carbapenemase VIM-1 / Metallo-beta-lactamase / Metallo-beta-lactamase VIM-1 / Metallobeta- ...Class B carbapenemase VIM-1 / Metallo-beta-lactamase / Metallo-beta-lactamase VIM-1 / Metallobeta-lactamase / Subclass B1 metallo-beta-lactamase VIM-1 / VIM-1 / VIM-1 metallo-beta-lactamase / VIM-1 protein


Mass: 28051.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaVIM, blaVIM-1, CAZ10_38240, CAZ10_38245 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q9XAY4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-YL9 / 7-[(1~{S})-1-[5-(2-azanylethyl)-2-oxidanylidene-1,3-oxazolidin-3-yl]ethyl]-3-[3-fluoranyl-4-(methylsulfonylmethyl)phenyl]-1~{H}-indole-2-carboxylic acid


Mass: 503.543 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26FN3O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 1.93 Å3/Da / Density % sol: 36.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.2M ammonium phosphate 0.1M TrisHCl, pH 8.5 / PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.26→34.63 Å / Num. obs: 56182 / % possible obs: 97.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 13.09 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.018 / Rrim(I) all: 0.047 / Net I/σ(I): 19.7
Reflection shellResolution: 1.26→1.29 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3321 / CC1/2: 0.85 / Rpim(I) all: 0.277 / Rrim(I) all: 0.61 / % possible all: 79.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.26→34.63 Å / SU ML: 0.1079 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.1207
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1536 2936 5.23 %
Rwork0.1408 53168 -
obs0.1415 56104 97.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.34 Å2
Refinement stepCycle: LAST / Resolution: 1.26→34.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1725 0 37 348 2110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00932049
X-RAY DIFFRACTIONf_angle_d1.25662838
X-RAY DIFFRACTIONf_chiral_restr0.0933312
X-RAY DIFFRACTIONf_plane_restr0.0156378
X-RAY DIFFRACTIONf_dihedral_angle_d24.7983338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.280.2324890.22831979X-RAY DIFFRACTION77.14
1.28-1.30.29751170.24312198X-RAY DIFFRACTION84
1.3-1.330.21941440.19882486X-RAY DIFFRACTION97.59
1.33-1.350.20151470.17172590X-RAY DIFFRACTION99.89
1.35-1.380.151420.14912568X-RAY DIFFRACTION99.93
1.38-1.410.16091670.13542565X-RAY DIFFRACTION99.96
1.41-1.440.16121350.13422589X-RAY DIFFRACTION99.96
1.44-1.480.15721630.13622551X-RAY DIFFRACTION99.78
1.48-1.520.15661390.12022587X-RAY DIFFRACTION99.89
1.52-1.560.13021320.12622580X-RAY DIFFRACTION99.96
1.56-1.610.13361300.12582595X-RAY DIFFRACTION99.71
1.61-1.670.13761350.12672571X-RAY DIFFRACTION99.82
1.67-1.740.1571480.12072585X-RAY DIFFRACTION99.85
1.74-1.820.14531230.12432615X-RAY DIFFRACTION99.78
1.82-1.910.1281260.12482566X-RAY DIFFRACTION99.37
1.91-2.030.14981320.12642591X-RAY DIFFRACTION99.09
2.03-2.190.13751440.12162593X-RAY DIFFRACTION99.27
2.19-2.410.13771520.12552539X-RAY DIFFRACTION99.19
2.41-2.760.14531630.13692570X-RAY DIFFRACTION99.85
2.76-3.480.14671500.14432620X-RAY DIFFRACTION100
3.48-34.630.17261580.16372630X-RAY DIFFRACTION99.68

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