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- PDB-8pac: Crystal structure of the metallo-beta-lactamase VIM1 with 2553 -

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Basic information

Entry
Database: PDB / ID: 8pac
TitleCrystal structure of the metallo-beta-lactamase VIM1 with 2553
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: 1.1 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 2553
Authors: Calvopina, K. / Brem, J. / Farley, A.J.M. / Allen, M.D. / Schofield, C.J.
History
DepositionJun 7, 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

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase VIM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6974
Polymers28,0511
Non-polymers6453
Water6,089338
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.530, 67.960, 40.290
Angle α, β, γ (deg.)90.000, 93.450, 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-XNE / 7-[(1~{S})-1-[4-(aminomethyl)phenyl]carbonyloxyethyl]-3-[6-(morpholin-4-ylmethyl)pyridin-3-yl]-1~{H}-indole-2-carboxylic acid


Mass: 514.572 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H30N4O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 1.93 Å3/Da / Density % sol: 36.13 %
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: 0.97872 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.1→39.46 Å / Num. obs: 84239 / % possible obs: 98 % / Redundancy: 5.7 % / Biso Wilson estimate: 11.78 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.019 / Rrim(I) all: 0.049 / Net I/σ(I): 16.8
Reflection shellResolution: 1.1→1.13 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 5415 / CC1/2: 0.847 / Rpim(I) all: 0.24 / Rrim(I) all: 0.471 / % possible all: 85.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→34.61 Å / SU ML: 0.0783 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.4685
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1336 4392 5.22 %
Rwork0.1207 79811 -
obs0.1213 84203 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.81 Å2
Refinement stepCycle: LAST / Resolution: 1.1→34.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 40 338 2109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01982040
X-RAY DIFFRACTIONf_angle_d1.64512820
X-RAY DIFFRACTIONf_chiral_restr0.1207311
X-RAY DIFFRACTIONf_plane_restr0.0159383
X-RAY DIFFRACTIONf_dihedral_angle_d17.8273330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.21081170.17662219X-RAY DIFFRACTION81.99
1.11-1.130.21051200.17972363X-RAY DIFFRACTION87.09
1.13-1.140.17631370.14422526X-RAY DIFFRACTION92.66
1.14-1.150.15491250.11922590X-RAY DIFFRACTION95.63
1.15-1.170.15171320.11422643X-RAY DIFFRACTION96.86
1.17-1.180.13221820.11172644X-RAY DIFFRACTION98.26
1.18-1.20.12911290.11252653X-RAY DIFFRACTION98.44
1.2-1.220.17371460.11532685X-RAY DIFFRACTION98.16
1.22-1.240.19111620.14472679X-RAY DIFFRACTION98.89
1.24-1.260.13691590.1032660X-RAY DIFFRACTION98.81
1.26-1.280.11811530.10462639X-RAY DIFFRACTION98.66
1.28-1.30.21231540.14712679X-RAY DIFFRACTION98.54
1.3-1.330.14561310.10772700X-RAY DIFFRACTION99.3
1.33-1.360.12531390.0952735X-RAY DIFFRACTION99.24
1.36-1.390.12051480.08642692X-RAY DIFFRACTION99.3
1.39-1.420.12641550.08912674X-RAY DIFFRACTION99.33
1.42-1.450.10621450.08622685X-RAY DIFFRACTION99.33
1.45-1.490.11591940.09272689X-RAY DIFFRACTION99.62
1.49-1.540.11421700.08362658X-RAY DIFFRACTION99.54
1.54-1.590.10971360.08462709X-RAY DIFFRACTION99.55
1.59-1.640.1181460.08382722X-RAY DIFFRACTION99.65
1.64-1.710.10851100.0922772X-RAY DIFFRACTION99.93
1.71-1.790.12171430.09252706X-RAY DIFFRACTION99.75
1.79-1.880.11851180.10272761X-RAY DIFFRACTION99.9
1.88-20.13511220.11752718X-RAY DIFFRACTION99.44
2-2.150.11961560.10782716X-RAY DIFFRACTION99.79
2.15-2.370.12891980.12562674X-RAY DIFFRACTION99.55
2.37-2.710.13621190.1262768X-RAY DIFFRACTION99.9
2.71-3.420.13411980.13852694X-RAY DIFFRACTION99.79
3.42-34.610.14411480.15492758X-RAY DIFFRACTION99.11

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