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- PDB-8pgu: Crystal structure of the metallo-beta-lactamase VIM1 with 3394 -

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Basic information

Entry
Database: PDB / ID: 8pgu
TitleCrystal structure of the metallo-beta-lactamase VIM1 with 3394
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: 1.62 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 3394
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)28,6194
Polymers28,0511
Non-polymers5673
Water6,161342
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-81 kcal/mol
Surface area9640 Å2
Unit cell
Length a, b, c (Å)39.420, 67.880, 40.260
Angle α, β, γ (deg.)90.000, 93.540, 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-YUH / 7-[(1~{S})-1-[2-(aminomethyl)-6-oxidanylidene-5-oxa-7-azaspiro[3.4]octan-7-yl]ethyl]-3-(6-oxidanylidene-1~{H}-pyridin-3-yl)-1~{H}-indole-2-carboxylic acid


Mass: 436.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H24N4O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 35.82 %
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: 0.81564 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81564 Å / Relative weight: 1
ReflectionResolution: 1.62→34.58 Å / Num. obs: 26808 / % possible obs: 99.4 % / Redundancy: 7.1 % / Biso Wilson estimate: 15.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.036 / Rrim(I) all: 0.095 / Net I/σ(I): 13.5
Reflection shellResolution: 1.62→1.66 Å / Redundancy: 7 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1973 / CC1/2: 0.764 / Rpim(I) all: 0.316 / Rrim(I) all: 0.842 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→34.58 Å / SU ML: 0.1674 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.3031
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1862 1349 5.04 %
Rwork0.1614 25435 -
obs0.1626 26784 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.91 Å2
Refinement stepCycle: LAST / Resolution: 1.62→34.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 34 342 2107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00271993
X-RAY DIFFRACTIONf_angle_d0.63442757
X-RAY DIFFRACTIONf_chiral_restr0.047310
X-RAY DIFFRACTIONf_plane_restr0.0097372
X-RAY DIFFRACTIONf_dihedral_angle_d9.1568304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.680.29771330.22972543X-RAY DIFFRACTION100
1.68-1.750.21281270.19262554X-RAY DIFFRACTION100
1.75-1.820.21161360.17422554X-RAY DIFFRACTION100
1.82-1.920.26111150.19842538X-RAY DIFFRACTION98.81
1.92-2.040.17631340.15512501X-RAY DIFFRACTION98.69
2.04-2.20.16891610.14592527X-RAY DIFFRACTION99.89
2.2-2.420.21671330.16722481X-RAY DIFFRACTION96.99
2.42-2.770.17591370.14952555X-RAY DIFFRACTION99.81
2.77-3.490.16351330.15132567X-RAY DIFFRACTION99.93
3.49-34.580.16561400.1542615X-RAY DIFFRACTION99.82

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