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- PDB-8pgn: Crystal structure of the metallo-beta-lactamase VIM1 with 3169 -

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Basic information

Entry
Database: PDB / ID: 8pgn
TitleCrystal structure of the metallo-beta-lactamase VIM1 with 3169
ComponentsBeta-lactamase VIM-1
KeywordsANTIMICROBIAL PROTEIN / Complex / metallo-beta-lactamase / inhibitor / zinc / indole carboxylate
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / hydrolase activity / 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
: / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 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 3169
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)28,7284
Polymers28,0511
Non-polymers6763
Water6,089338
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 area9410 Å2
Unit cell
Length a, b, c (Å)39.430, 67.950, 40.250
Angle α, β, γ (deg.)90.000, 93.400, 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-YRF / 7-[(1~{S})-1-[5-[(3-azanylazetidin-1-yl)methyl]-2-oxidanylidene-1,3-oxazolidin-3-yl]ethyl]-3-[3-fluoranyl-4-(methylsulfonylamino)phenyl]-1~{H}-indole-2-carboxylic acid


Mass: 545.583 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H28FN5O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: I24 / Wavelength: 0.96864 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96864 Å / Relative weight: 1
ReflectionResolution: 1.12→40.18 Å / Num. obs: 79201 / % possible obs: 97.6 % / Redundancy: 5.8 % / Biso Wilson estimate: 11.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.014 / Rrim(I) all: 0.036 / Net I/σ(I): 24.5
Reflection shellResolution: 1.12→1.15 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 5.9 / Num. unique obs: 4709 / CC1/2: 0.965 / Rpim(I) all: 0.102 / Rrim(I) all: 0.204 / % possible all: 79.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.12→40.18 Å / SU ML: 0.0611 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.3686
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1397 4029 5.09 %
Rwork0.1206 75145 -
obs0.1216 79174 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.46 Å2
Refinement stepCycle: LAST / Resolution: 1.12→40.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 40 338 2109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01812048
X-RAY DIFFRACTIONf_angle_d1.63762838
X-RAY DIFFRACTIONf_chiral_restr0.1193314
X-RAY DIFFRACTIONf_plane_restr0.018384
X-RAY DIFFRACTIONf_dihedral_angle_d21.9564321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.12-1.130.1341180.12521962X-RAY DIFFRACTION75.06
1.13-1.150.15361040.11812192X-RAY DIFFRACTION82.68
1.15-1.160.12441080.10942322X-RAY DIFFRACTION86.35
1.16-1.180.13531120.10892464X-RAY DIFFRACTION93.06
1.18-1.190.14471260.10442558X-RAY DIFFRACTION95.28
1.19-1.210.14671240.10332636X-RAY DIFFRACTION99.17
1.21-1.230.14431300.10012638X-RAY DIFFRACTION99.28
1.23-1.250.12811250.09722619X-RAY DIFFRACTION99.35
1.25-1.270.13091610.09622641X-RAY DIFFRACTION99.47
1.27-1.290.14561360.10752633X-RAY DIFFRACTION99.43
1.29-1.310.11331260.10352679X-RAY DIFFRACTION99.68
1.31-1.340.12111420.09862632X-RAY DIFFRACTION99.71
1.34-1.370.11071510.0942631X-RAY DIFFRACTION99.78
1.37-1.40.12171420.09522648X-RAY DIFFRACTION99.96
1.4-1.430.11551580.09252635X-RAY DIFFRACTION99.96
1.43-1.460.13191440.09162682X-RAY DIFFRACTION99.96
1.46-1.50.10531390.09222628X-RAY DIFFRACTION99.93
1.5-1.550.10911370.09292663X-RAY DIFFRACTION100
1.55-1.60.12211620.09512628X-RAY DIFFRACTION99.93
1.6-1.650.1141660.09882650X-RAY DIFFRACTION99.93
1.65-1.720.12661410.10122649X-RAY DIFFRACTION99.93
1.72-1.80.13261700.10322631X-RAY DIFFRACTION99.79
1.8-1.890.12481390.10762678X-RAY DIFFRACTION99.93
1.89-2.010.12281240.10912673X-RAY DIFFRACTION99.89
2.01-2.170.13281380.11392649X-RAY DIFFRACTION99.93
2.17-2.390.13581300.12012694X-RAY DIFFRACTION100
2.39-2.730.13411780.13242642X-RAY DIFFRACTION99.89
2.73-3.440.15971270.14392700X-RAY DIFFRACTION99.93
3.44-40.180.17471710.15792688X-RAY DIFFRACTION99.65

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