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- PDB-8pb0: Crystal structure of the metallo-beta-lactamase VIM1 with 2696 -

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Basic information

Entry
Database: PDB / ID: 8pb0
TitleCrystal structure of the metallo-beta-lactamase VIM1 with 2696
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: 1.26 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 2696
Authors: Calvopina, K. / Brem, J. / Farley, A.J.M. / Allen, M.D. / Schofield, C.J.
History
DepositionJun 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 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)28,7414
Polymers28,0511
Non-polymers6893
Water5,855325
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 area9400 Å2
Unit cell
Length a, b, c (Å)39.490, 67.910, 40.220
Angle α, β, γ (deg.)90.000, 93.370, 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-XQE / 7-[(1~{S})-1-[4-[[[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]amino]methyl]-1,2,3-triazol-1-yl]ethyl]-3-[3-fluoranyl-4-(methylsulfonylmethyl)phenyl]-1~{H}-indole-2-carboxylic acid


Mass: 558.582 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H27FN6O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 35.91 %
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: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.26→28.99 Å / Num. obs: 56158 / % possible obs: 98.3 % / Redundancy: 6.3 % / Biso Wilson estimate: 12.87 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.031 / Rrim(I) all: 0.08 / Net I/σ(I): 13
Reflection shellResolution: 1.26→1.29 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3609 / CC1/2: 0.677 / Rpim(I) all: 0.47 / Rrim(I) all: 0.989 / % possible all: 85.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.26→28.99 Å / SU ML: 0.097 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.6229
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1603 2774 4.94 %
Rwork0.1347 53329 -
obs0.1359 56103 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.98 Å2
Refinement stepCycle: LAST / Resolution: 1.26→28.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 41 325 2097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01032107
X-RAY DIFFRACTIONf_angle_d1.26532921
X-RAY DIFFRACTIONf_chiral_restr0.0943323
X-RAY DIFFRACTIONf_plane_restr0.0179391
X-RAY DIFFRACTIONf_dihedral_angle_d21.9484347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.280.24211100.21552256X-RAY DIFFRACTION83.4
1.28-1.310.3061320.26932459X-RAY DIFFRACTION90.94
1.31-1.330.23381390.16912654X-RAY DIFFRACTION98.1
1.33-1.360.18371600.14672673X-RAY DIFFRACTION99.44
1.36-1.390.22031490.14572709X-RAY DIFFRACTION99.55
1.39-1.420.15341520.12222678X-RAY DIFFRACTION100
1.42-1.450.18031470.12382677X-RAY DIFFRACTION99.86
1.45-1.490.17461180.12772719X-RAY DIFFRACTION99.79
1.49-1.540.14981580.11222706X-RAY DIFFRACTION99.58
1.54-1.590.1521670.10552664X-RAY DIFFRACTION99.96
1.59-1.640.1391530.10182719X-RAY DIFFRACTION99.97
1.64-1.710.13931360.10442714X-RAY DIFFRACTION99.93
1.71-1.790.12741280.10632725X-RAY DIFFRACTION99.93
1.79-1.880.14631340.11142709X-RAY DIFFRACTION99.93
1.88-20.15391290.14012635X-RAY DIFFRACTION96.68
2-2.150.13431540.11632694X-RAY DIFFRACTION99.65
2.15-2.370.16371240.13042660X-RAY DIFFRACTION97.1
2.37-2.710.1631470.12572728X-RAY DIFFRACTION99.97
2.71-3.420.14121020.13892775X-RAY DIFFRACTION99.9
3.42-28.990.1691350.1552775X-RAY DIFFRACTION99.66

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