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- PDB-8pgf: Crystal structure of the metallo-beta-lactamase VIM1 with 2941 -

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Basic information

Entry
Database: PDB / ID: 8pgf
TitleCrystal structure of the metallo-beta-lactamase VIM1 with 2941
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: 1.2 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 2941
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)28,6964
Polymers28,0511
Non-polymers6443
Water6,918384
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 area9570 Å2
Unit cell
Length a, b, c (Å)39.497, 67.627, 40.267
Angle α, β, γ (deg.)90.000, 93.530, 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-XMU / 7-[(1~{S})-1-[[4-(aminomethyl)phenyl]carbonylamino]ethyl]-3-[6-(morpholin-4-ylmethyl)pyridin-3-yl]-1~{H}-indole-2-carboxylic acid


Mass: 513.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H31N5O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 35.72 %
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: 0.979499 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979499 Å / Relative weight: 1
ReflectionResolution: 1.2→29.05 Å / Num. obs: 62636 / % possible obs: 94.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 13.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.012 / Rrim(I) all: 0.032 / Net I/σ(I): 35.7
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 2067 / CC1/2: 0.961 / Rpim(I) all: 0.115 / Rrim(I) all: 0.213 / % possible all: 63.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→29.05 Å / SU ML: 0.0679 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.1764
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1362 6039 4.94 %
Rwork0.1165 116140 -
obs0.1174 61090 93.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.8 Å2
Refinement stepCycle: LAST / Resolution: 1.2→29.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 40 384 2155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02162051
X-RAY DIFFRACTIONf_angle_d1.64012838
X-RAY DIFFRACTIONf_chiral_restr0.1347315
X-RAY DIFFRACTIONf_plane_restr0.019385
X-RAY DIFFRACTIONf_dihedral_angle_d19.7206327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.210.1533930.13932237X-RAY DIFFRACTION53.55
1.21-1.230.15291270.13072688X-RAY DIFFRACTION64.15
1.23-1.240.13981580.12192940X-RAY DIFFRACTION71.96
1.24-1.260.14741730.11893179X-RAY DIFFRACTION77.06
1.26-1.270.13621980.11323466X-RAY DIFFRACTION84.23
1.27-1.290.19131590.10873849X-RAY DIFFRACTION92.71
1.29-1.310.16111720.10913919X-RAY DIFFRACTION94.52
1.31-1.330.13552280.09954038X-RAY DIFFRACTION97.09
1.33-1.350.13642500.09424001X-RAY DIFFRACTION97.68
1.35-1.370.11732190.08923992X-RAY DIFFRACTION97.59
1.37-1.40.13711860.08814121X-RAY DIFFRACTION99.06
1.4-1.420.12232200.094003X-RAY DIFFRACTION98.28
1.42-1.450.12182490.0914090X-RAY DIFFRACTION99.15
1.45-1.480.15492340.08884056X-RAY DIFFRACTION98.73
1.48-1.510.12032420.08574097X-RAY DIFFRACTION99.34
1.51-1.550.11912180.08594070X-RAY DIFFRACTION99.08
1.55-1.580.11841680.08584127X-RAY DIFFRACTION99.31
1.58-1.630.13312500.08914085X-RAY DIFFRACTION99.63
1.63-1.680.12871990.08984149X-RAY DIFFRACTION99.56
1.68-1.730.11591750.09364105X-RAY DIFFRACTION99.44
1.73-1.790.12342180.10034113X-RAY DIFFRACTION99.75
1.79-1.860.12191950.10054160X-RAY DIFFRACTION99.86
1.86-1.950.11031750.10394163X-RAY DIFFRACTION99.4
1.95-2.050.13091770.10164074X-RAY DIFFRACTION99.53
2.05-2.180.12722430.10994156X-RAY DIFFRACTION99.35
2.18-2.350.1161820.10974124X-RAY DIFFRACTION99.19
2.35-2.580.14232490.11934049X-RAY DIFFRACTION100
2.58-2.960.13443020.1324049X-RAY DIFFRACTION99.84
2.96-3.720.15512020.13224133X-RAY DIFFRACTION99.75
3.72-29.050.15511780.15743907X-RAY DIFFRACTION93.8

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