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- PDB-8pga: Crystal structure of the metallo-beta-lactamase VIM1 with 2818 -

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Basic information

Entry
Database: PDB / ID: 8pga
TitleCrystal structure of the metallo-beta-lactamase VIM1 with 2818
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: 1.19 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 2818
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)28,7004
Polymers28,0511
Non-polymers6483
Water6,648369
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 area9460 Å2
Unit cell
Length a, b, c (Å)39.420, 67.930, 40.300
Angle α, β, γ (deg.)90.000, 94.020, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 35.9 %
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: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.19→39.32 Å / Num. obs: 65722 / % possible obs: 97 % / Redundancy: 6.8 % / Biso Wilson estimate: 11.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.037 / Rrim(I) all: 0.098 / Net I/σ(I): 10.5
Reflection shellResolution: 1.19→1.22 Å / Rmerge(I) obs: 0.788 / Mean I/σ(I) obs: 2 / Num. unique obs: 4711 / CC1/2: 0.801 / Rpim(I) all: 0.329 / Rrim(I) all: 0.855

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.19→34.6 Å / SU ML: 0.0856 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.7118
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1464 3321 5.05 %
Rwork0.1266 62393 -
obs0.1275 65714 96.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.99 Å2
Refinement stepCycle: LAST / Resolution: 1.19→34.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 38 369 2138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112094
X-RAY DIFFRACTIONf_angle_d1.28772901
X-RAY DIFFRACTIONf_chiral_restr0.0991317
X-RAY DIFFRACTIONf_plane_restr0.014391
X-RAY DIFFRACTIONf_dihedral_angle_d13.8591364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.19-1.210.20991290.19082507X-RAY DIFFRACTION94.89
1.21-1.230.21281260.18532553X-RAY DIFFRACTION94.73
1.23-1.240.23941310.182557X-RAY DIFFRACTION94.95
1.24-1.260.21141220.17522557X-RAY DIFFRACTION95.07
1.26-1.290.20281360.16932527X-RAY DIFFRACTION95.18
1.29-1.310.21911430.15662533X-RAY DIFFRACTION95.54
1.31-1.330.18491380.15012578X-RAY DIFFRACTION95.77
1.33-1.360.18151440.14082537X-RAY DIFFRACTION95.75
1.36-1.390.16361500.13642544X-RAY DIFFRACTION96.01
1.39-1.420.16471470.12562585X-RAY DIFFRACTION96.4
1.42-1.460.15151390.12722588X-RAY DIFFRACTION96.63
1.46-1.50.18161440.12232561X-RAY DIFFRACTION96.75
1.5-1.540.16811400.11722610X-RAY DIFFRACTION96.93
1.54-1.590.13411250.11542609X-RAY DIFFRACTION97.23
1.59-1.650.16851310.11562617X-RAY DIFFRACTION97.34
1.65-1.720.15441540.10822601X-RAY DIFFRACTION97.8
1.72-1.790.13991760.10642596X-RAY DIFFRACTION97.99
1.79-1.890.13061520.10172609X-RAY DIFFRACTION98.05
1.89-2.010.11891630.09872642X-RAY DIFFRACTION98.52
2.01-2.160.12421390.10592638X-RAY DIFFRACTION98.9
2.16-2.380.121260.11052670X-RAY DIFFRACTION98.87
2.38-2.720.14361050.11932730X-RAY DIFFRACTION99.2
2.72-3.430.12131410.13092686X-RAY DIFFRACTION99.65
3.43-34.60.14661200.14752758X-RAY DIFFRACTION99.48

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