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- PDB-8pgk: Crystal structure of the metallo-beta-lactamase VIM1 with 3016 -

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Basic information

Entry
Database: PDB / ID: 8pgk
TitleCrystal structure of the metallo-beta-lactamase VIM1 with 3016
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 3016
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)28,7264
Polymers28,0511
Non-polymers6743
Water6,503361
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-80 kcal/mol
Surface area9570 Å2
Unit cell
Length a, b, c (Å)39.490, 67.890, 40.300
Angle α, β, γ (deg.)90.000, 93.850, 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-YVH / 7-[(1~{S})-1-(2-carbamimidoyl-6-oxidanylidene-5-oxa-2,7-diazaspiro[3.4]octan-7-yl)ethyl]-3-[3-fluoranyl-4-(methylsulfonylmethyl)phenyl]-1~{H}-indole-2-carboxylic acid


Mass: 543.567 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H26FN5O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 35.99 %
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: Nov 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.24→34.08 Å / Num. obs: 57167 / % possible obs: 95.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 13.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.019 / Rrim(I) all: 0.05 / Net I/σ(I): 18.5
Reflection shellResolution: 1.24→1.27 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3151 / CC1/2: 0.749 / Rpim(I) all: 0.311 / Rrim(I) all: 0.736 / % possible all: 71.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.24→29.14 Å / SU ML: 0.1059 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.7783
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1508 2855 5 %
Rwork0.1338 54302 -
obs0.1346 57157 95.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.47 Å2
Refinement stepCycle: LAST / Resolution: 1.24→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 40 361 2132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01161992
X-RAY DIFFRACTIONf_angle_d1.37442761
X-RAY DIFFRACTIONf_chiral_restr0.0982304
X-RAY DIFFRACTIONf_plane_restr0.0197366
X-RAY DIFFRACTIONf_dihedral_angle_d6.1334345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.24-1.260.2651850.19361953X-RAY DIFFRACTION67.71
1.26-1.280.18541150.18082296X-RAY DIFFRACTION81.1
1.28-1.310.2351510.20582622X-RAY DIFFRACTION92.8
1.31-1.340.19831500.15252731X-RAY DIFFRACTION95.65
1.34-1.360.18541300.14582737X-RAY DIFFRACTION96.31
1.36-1.40.19931360.12872747X-RAY DIFFRACTION96.65
1.4-1.430.14531550.11722734X-RAY DIFFRACTION96.69
1.43-1.470.14771540.11492732X-RAY DIFFRACTION97.01
1.47-1.510.13121440.11152787X-RAY DIFFRACTION97.18
1.51-1.560.12551620.10462750X-RAY DIFFRACTION97.49
1.56-1.620.14321650.10922759X-RAY DIFFRACTION97.6
1.62-1.680.14541690.11232775X-RAY DIFFRACTION98.1
1.68-1.760.1441510.11282801X-RAY DIFFRACTION98.27
1.76-1.850.1461410.11552797X-RAY DIFFRACTION98.46
1.85-1.970.16931500.12632766X-RAY DIFFRACTION97.17
1.97-2.120.13191370.11852845X-RAY DIFFRACTION98.84
2.12-2.330.13921610.12632800X-RAY DIFFRACTION98.27
2.33-2.670.13621620.12412830X-RAY DIFFRACTION99.67
2.67-3.360.14361210.14112905X-RAY DIFFRACTION99.84
3.36-29.140.16291160.15752935X-RAY DIFFRACTION99.61

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