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- PDB-8pg2: Crystal structure of the metallo-beta-lactamase VIM1 with 2728 -

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Basic information

Entry
Database: PDB / ID: 8pg2
TitleCrystal structure of the metallo-beta-lactamase VIM1 with 2728
ComponentsBeta-lactamase VIM-1
KeywordsANTIMICROBIAL PROTEIN / Complex / metallo-beta-lactamase / inhibitor / zinc / indole carboxylate
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
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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 2728
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,7785
Polymers28,0511
Non-polymers7274
Water7,026390
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-77 kcal/mol
Surface area9330 Å2
Unit cell
Length a, b, c (Å)39.548, 67.957, 40.341
Angle α, β, γ (deg.)90.000, 93.520, 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-YLH / 7-[(1~{S})-1-[5-(3-azanylpropyl)-2-oxidanylidene-1,3-oxazolidin-3-yl]ethyl]-3-[3-fluoranyl-4-(methylsulfonylmethyl)phenyl]-1~{H}-indole-2-carboxylic acid


Mass: 517.570 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H28FN3O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 36.23 %
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: 0.9762 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: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.25→29.09 Å / Num. obs: 57553 / % possible obs: 97.3 % / Redundancy: 6.4 % / Biso Wilson estimate: 12.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.014 / Rrim(I) all: 0.036 / Net I/σ(I): 34.9
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.103 / Mean I/σ(I) obs: 10 / Num. unique obs: 2244 / CC1/2: 0.987 / Rpim(I) all: 0.058 / Rrim(I) all: 0.119 / % possible all: 76.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→29.09 Å / SU ML: 0.078 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 10.4619
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1311 5659 5.02 %
Rwork0.1122 107029 -
obs0.1131 56348 96.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.95 Å2
Refinement stepCycle: LAST / Resolution: 1.25→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 42 390 2163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02182086
X-RAY DIFFRACTIONf_angle_d1.68062889
X-RAY DIFFRACTIONf_chiral_restr0.12317
X-RAY DIFFRACTIONf_plane_restr0.0198385
X-RAY DIFFRACTIONf_dihedral_angle_d17.8485347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.260.15361140.11712627X-RAY DIFFRACTION69.45
1.26-1.280.14361650.10463021X-RAY DIFFRACTION82.52
1.28-1.290.12781500.10423233X-RAY DIFFRACTION87.48
1.29-1.310.15941880.11523287X-RAY DIFFRACTION89.1
1.31-1.330.13932120.09563515X-RAY DIFFRACTION96.68
1.33-1.340.11571890.0963671X-RAY DIFFRACTION98.85
1.34-1.360.11631680.09673730X-RAY DIFFRACTION98.73
1.36-1.380.15191700.09543646X-RAY DIFFRACTION99.84
1.38-1.410.1461910.09393723X-RAY DIFFRACTION99.75
1.41-1.430.12132050.09433655X-RAY DIFFRACTION99.9
1.43-1.450.1282220.09373680X-RAY DIFFRACTION99.82
1.45-1.480.1142150.09553664X-RAY DIFFRACTION99.36
1.48-1.510.12271930.08913686X-RAY DIFFRACTION99.9
1.51-1.540.12991880.09213672X-RAY DIFFRACTION99.79
1.54-1.570.11832350.0923672X-RAY DIFFRACTION99.64
1.57-1.610.12321950.08943686X-RAY DIFFRACTION99.56
1.61-1.650.11352380.09133629X-RAY DIFFRACTION99.59
1.65-1.690.12632140.09593598X-RAY DIFFRACTION99.71
1.69-1.740.11892030.09043701X-RAY DIFFRACTION99.69
1.74-1.80.11961940.09173681X-RAY DIFFRACTION99.54
1.8-1.860.11822150.10323670X-RAY DIFFRACTION99.59
1.86-1.940.14091860.09723613X-RAY DIFFRACTION98.09
1.94-2.030.13151660.09623718X-RAY DIFFRACTION99.21
2.03-2.130.1181860.10113639X-RAY DIFFRACTION98.86
2.13-2.270.1242050.10483525X-RAY DIFFRACTION96.43
2.27-2.440.12852310.10783631X-RAY DIFFRACTION99.08
2.44-2.690.1331880.12073682X-RAY DIFFRACTION99.49
2.69-3.080.16111460.13023740X-RAY DIFFRACTION99.54
3.08-3.870.13671710.12513640X-RAY DIFFRACTION98.5
3.88-29.090.14081160.15593394X-RAY DIFFRACTION90.12

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