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- PDB-8pgm: Crystal structure of the metallo-beta-lactamase VIM1 with 3062 -

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Basic information

Entry
Database: PDB / ID: 8pgm
TitleCrystal structure of the metallo-beta-lactamase VIM1 with 3062
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: 1.27 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 3062
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)28,6515
Polymers28,0511
Non-polymers5994
Water5,152286
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-76 kcal/mol
Surface area9570 Å2
Unit cell
Length a, b, c (Å)39.420, 67.830, 40.080
Angle α, β, γ (deg.)90.000, 93.280, 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-YU0 / 3-[4-[(azanyl-methyl-oxidanyl-$l^{4}-sulfanyl)methyl]-3-fluoranyl-phenyl]-7-propan-2-yl-1~{H}-indole-2-carboxylic acid


Mass: 390.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23FN2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 1.91 Å3/Da / Density % sol: 35.5 %
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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.27→34.04 Å / Num. obs: 54022 / % possible obs: 97.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 14.74 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.021 / Rrim(I) all: 0.055 / Net I/σ(I): 16.2
Reflection shellResolution: 1.27→1.3 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.869 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3620 / CC1/2: 0.708 / Rpim(I) all: 0.395 / Rrim(I) all: 0.959 / % possible all: 89.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.27→28.9 Å / SU ML: 0.1266 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.4397
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1558 2674 4.95 %
Rwork0.1282 51331 -
obs0.1295 54005 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.38 Å2
Refinement stepCycle: LAST / Resolution: 1.27→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 33 286 2050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01322034
X-RAY DIFFRACTIONf_angle_d1.50282817
X-RAY DIFFRACTIONf_chiral_restr0.1086313
X-RAY DIFFRACTIONf_plane_restr0.0137376
X-RAY DIFFRACTIONf_dihedral_angle_d12.957325
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.290.32031240.25582392X-RAY DIFFRACTION87.54
1.29-1.320.23151330.21172600X-RAY DIFFRACTION94.21
1.32-1.340.23851500.1772672X-RAY DIFFRACTION96.28
1.34-1.370.20081680.15222644X-RAY DIFFRACTION96.67
1.37-1.410.19291410.13722682X-RAY DIFFRACTION96.88
1.41-1.440.14291540.12352646X-RAY DIFFRACTION96.82
1.44-1.480.18471210.11612724X-RAY DIFFRACTION97.4
1.48-1.520.16211480.11242693X-RAY DIFFRACTION97.49
1.52-1.570.16051620.1112678X-RAY DIFFRACTION97.76
1.57-1.630.16271610.10952682X-RAY DIFFRACTION98.2
1.63-1.690.15521340.10662733X-RAY DIFFRACTION98.02
1.69-1.770.14381270.10372734X-RAY DIFFRACTION98.62
1.77-1.860.12751290.10182768X-RAY DIFFRACTION98.84
1.86-1.980.1251390.10512737X-RAY DIFFRACTION98.83
1.98-2.130.12521560.1072733X-RAY DIFFRACTION99.01
2.13-2.350.17211320.11192779X-RAY DIFFRACTION98.95
2.35-2.690.1531500.12132776X-RAY DIFFRACTION99.76
2.69-3.390.16011070.13612830X-RAY DIFFRACTION99.9
3.39-28.90.14981380.15032828X-RAY DIFFRACTION99.5

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