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- PDB-8pgq: Crystal structure of the metallo-beta-lactamase VIM1 with 3225 -

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Basic information

Entry
Database: PDB / ID: 8pgq
TitleCrystal structure of the metallo-beta-lactamase VIM1 with 3225
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: 1.24 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 3225
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)28,7204
Polymers28,0511
Non-polymers6683
Water6,251347
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 area9540 Å2
Unit cell
Length a, b, c (Å)39.520, 67.810, 40.230
Angle α, β, γ (deg.)90.000, 93.580, 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-YUC / 7-[(1~{S})-1-[2-(aminomethyl)-6-oxidanylidene-5-oxa-7-azaspiro[3.4]octan-7-yl]ethyl]-3-[3-cyano-4-(methylsulfonylamino)phenyl]-1~{H}-indole-2-carboxylic acid


Mass: 537.587 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H27N5O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 1.92 Å3/Da / Density % sol: 35.87 %
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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.24→34.55 Å / Num. obs: 58773 / % possible obs: 98.1 % / Redundancy: 6.4 % / Biso Wilson estimate: 12.02 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.026 / Rpim(I) all: 0.011 / Rrim(I) all: 0.028 / Net I/σ(I): 31.5
Reflection shellResolution: 1.24→1.27 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 7.5 / Num. unique obs: 3484 / CC1/2: 0.979 / Rpim(I) all: 0.073 / Rrim(I) all: 0.162 / % possible all: 78.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.24→29.06 Å / SU ML: 0.0869 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 10.6708
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.137 2954 5.03 %
Rwork0.1157 55784 -
obs0.1167 58738 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.85 Å2
Refinement stepCycle: LAST / Resolution: 1.24→29.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 40 347 2118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02152115
X-RAY DIFFRACTIONf_angle_d1.90032942
X-RAY DIFFRACTIONf_chiral_restr0.1386320
X-RAY DIFFRACTIONf_plane_restr0.0205396
X-RAY DIFFRACTIONf_dihedral_angle_d19.872373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.24-1.260.1257950.10122051X-RAY DIFFRACTION75.56
1.26-1.280.14791150.09852343X-RAY DIFFRACTION86.79
1.28-1.310.13351490.10182641X-RAY DIFFRACTION98.1
1.31-1.330.16121570.10022707X-RAY DIFFRACTION99.97
1.33-1.360.1331330.10612675X-RAY DIFFRACTION100
1.36-1.390.14421230.09822739X-RAY DIFFRACTION100
1.39-1.420.15161500.09482689X-RAY DIFFRACTION100
1.42-1.450.12411550.09232672X-RAY DIFFRACTION100
1.45-1.490.11921490.09912688X-RAY DIFFRACTION100
1.49-1.540.12071470.09112725X-RAY DIFFRACTION99.86
1.54-1.590.13611600.09772659X-RAY DIFFRACTION99.89
1.59-1.640.1311640.0972712X-RAY DIFFRACTION100
1.64-1.710.12671690.09652675X-RAY DIFFRACTION100
1.71-1.790.12381400.09812696X-RAY DIFFRACTION100
1.79-1.880.12721500.09862706X-RAY DIFFRACTION100
1.88-20.14681380.10072716X-RAY DIFFRACTION99.79
2-2.150.11421290.10242705X-RAY DIFFRACTION99.79
2.15-2.370.12441580.11022711X-RAY DIFFRACTION99.86
2.37-2.710.14781470.11752723X-RAY DIFFRACTION100
2.72-3.420.15051140.13352756X-RAY DIFFRACTION99.97
3.42-29.060.15181120.15032795X-RAY DIFFRACTION99.55

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