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- PDB-8pg5: Crystal structure of the metallo-beta-lactamase VIM1 with 2731 -

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Basic information

Entry
Database: PDB / ID: 8pg5
TitleCrystal structure of the metallo-beta-lactamase VIM1 with 2731
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: 1.25 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 2731
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)28,6714
Polymers28,0511
Non-polymers6193
Water6,828379
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 area9400 Å2
Unit cell
Length a, b, c (Å)39.515, 67.992, 40.245
Angle α, β, γ (deg.)90.000, 93.250, 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-YR8 / 3-[3-fluoranyl-4-(methylsulfonylmethyl)phenyl]-7-[(1~{S})-1-(piperidin-4-ylmethoxy)ethyl]-1~{H}-indole-2-carboxylic acid


Mass: 488.572 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H29FN2O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 36.08 %
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: 0.976254 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: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.25→28.98 Å / Num. obs: 56095 / % possible obs: 95.3 % / Redundancy: 6.5 % / Biso Wilson estimate: 11.19 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.026 / Rpim(I) all: 0.011 / Rrim(I) all: 0.028 / Net I/σ(I): 48.1
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 11.6 / Num. unique obs: 1932 / CC1/2: 0.979 / Rpim(I) all: 0.061 / Rrim(I) all: 0.13 / % possible all: 66.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→28.98 Å / SU ML: 0.0831 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 11.7984
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1404 5502 5.02 %
Rwork0.1173 104176 -
obs0.1184 54850 94.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.84 Å2
Refinement stepCycle: LAST / Resolution: 1.25→28.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 36 379 2146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01672064
X-RAY DIFFRACTIONf_angle_d1.59722860
X-RAY DIFFRACTIONf_chiral_restr0.1379316
X-RAY DIFFRACTIONf_plane_restr0.0152382
X-RAY DIFFRACTIONf_dihedral_angle_d19.8933355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.260.2175930.15842251X-RAY DIFFRACTION60.47
1.26-1.280.20221460.13582559X-RAY DIFFRACTION69.39
1.28-1.290.13891540.12522868X-RAY DIFFRACTION77.85
1.29-1.310.17021810.12673057X-RAY DIFFRACTION83.69
1.31-1.330.16151860.10573393X-RAY DIFFRACTION93.2
1.33-1.340.14551770.10313507X-RAY DIFFRACTION94.7
1.34-1.360.14751570.09783551X-RAY DIFFRACTION95.42
1.36-1.380.15171880.09753555X-RAY DIFFRACTION96.05
1.38-1.410.12581740.09753607X-RAY DIFFRACTION98.13
1.41-1.430.12992000.13564X-RAY DIFFRACTION97.92
1.43-1.450.15222130.10223580X-RAY DIFFRACTION97.33
1.45-1.480.1142080.10033567X-RAY DIFFRACTION96.97
1.48-1.510.12321770.09953595X-RAY DIFFRACTION98.41
1.51-1.540.14161900.09743640X-RAY DIFFRACTION98.1
1.54-1.570.14132380.09153583X-RAY DIFFRACTION98.53
1.57-1.610.13741900.09293653X-RAY DIFFRACTION98.61
1.61-1.650.12162370.09313576X-RAY DIFFRACTION98.91
1.65-1.690.13742120.09333532X-RAY DIFFRACTION98.63
1.69-1.740.09981980.09493688X-RAY DIFFRACTION98.78
1.74-1.80.12341840.09743643X-RAY DIFFRACTION99.15
1.8-1.860.12482170.1013621X-RAY DIFFRACTION99.12
1.86-1.940.1281860.10053596X-RAY DIFFRACTION98.21
1.94-2.030.12151690.09873696X-RAY DIFFRACTION98.82
2.03-2.130.13841830.10243606X-RAY DIFFRACTION98.06
2.13-2.270.12691990.10893573X-RAY DIFFRACTION97.72
2.27-2.440.13272260.11183615X-RAY DIFFRACTION99.12
2.44-2.690.14321950.12033652X-RAY DIFFRACTION99.3
2.69-3.080.18181380.13173721X-RAY DIFFRACTION99.28
3.08-3.880.14281680.13613644X-RAY DIFFRACTION99.17
3.88-28.980.17421180.16733483X-RAY DIFFRACTION92.64

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