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- PDB-8pg4: Crystal structure of the metallo-beta-lactamase VIM1 with 2730 -

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Basic information

Entry
Database: PDB / ID: 8pg4
TitleCrystal structure of the metallo-beta-lactamase VIM1 with 2730
ComponentsBeta-lactamase VIM-1
KeywordsANTIMICROBIAL PROTEIN / Complex / metallo-beta-lactamase / inhibitor / zinc / indole carboxylate
Function / homology: / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / metal ion binding / : / Beta-lactamase VIM-1
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 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 2730
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)28,6554
Polymers28,0511
Non-polymers6033
Water5,747319
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 area9270 Å2
Unit cell
Length a, b, c (Å)39.590, 68.100, 40.360
Angle α, β, γ (deg.)90.000, 93.320, 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-YTO / 3-[3-fluoranyl-4-(methylsulfonylmethyl)phenyl]-7-[(1~{R})-1-(1~{H}-1,2,3-triazol-5-ylmethoxy)ethyl]-1~{H}-indole-2-carboxylic acid


Mass: 472.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H21FN4O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 1.94 Å3/Da / Density % sol: 36.48 %
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 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.38→39.52 Å / Num. obs: 43095 / % possible obs: 98.2 % / Redundancy: 6.7 % / Biso Wilson estimate: 14.81 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.022 / Rrim(I) all: 0.057 / Net I/σ(I): 20
Reflection shellResolution: 1.38→1.42 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 3135 / CC1/2: 0.926 / Rpim(I) all: 0.183 / Rrim(I) all: 0.494 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.38→39.52 Å / SU ML: 0.1115 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.6158
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1626 2225 5.17 %
Rwork0.1432 40794 -
obs0.1442 43019 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.41 Å2
Refinement stepCycle: LAST / Resolution: 1.38→39.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1725 0 35 319 2079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01292056
X-RAY DIFFRACTIONf_angle_d1.44332850
X-RAY DIFFRACTIONf_chiral_restr0.1133313
X-RAY DIFFRACTIONf_plane_restr0.0198383
X-RAY DIFFRACTIONf_dihedral_angle_d23.8163338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.410.19091250.17872520X-RAY DIFFRACTION96.82
1.41-1.440.18881560.16932456X-RAY DIFFRACTION95.85
1.44-1.480.20921290.17462458X-RAY DIFFRACTION94.83
1.48-1.520.16991430.14252525X-RAY DIFFRACTION96.95
1.52-1.560.1461260.14342494X-RAY DIFFRACTION96.32
1.56-1.610.16391300.13392575X-RAY DIFFRACTION98.01
1.61-1.670.15381250.14082547X-RAY DIFFRACTION98.27
1.67-1.740.18921310.14092553X-RAY DIFFRACTION98.42
1.74-1.820.15971260.12982591X-RAY DIFFRACTION98.76
1.82-1.910.1631520.12952521X-RAY DIFFRACTION97.88
1.91-2.030.1491580.12712556X-RAY DIFFRACTION98.16
2.03-2.190.1431480.12682558X-RAY DIFFRACTION98.01
2.19-2.410.14711310.12432575X-RAY DIFFRACTION99.23
2.41-2.760.13311390.1372595X-RAY DIFFRACTION99.56
2.76-3.480.181540.14732614X-RAY DIFFRACTION99.89
3.48-39.520.17051520.16252656X-RAY DIFFRACTION99.79

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