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- PDB-8pb2: Crystal structure of the metallo-beta-lactamase VIM1 with 2697 -

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Basic information

Entry
Database: PDB / ID: 8pb2
TitleCrystal structure of the metallo-beta-lactamase VIM1 with 2697
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: 1.25 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 2697
Authors: Calvopina, K. / Brem, J. / Farley, A.J.M. / Allen, M.D. / Schofield, C.J.
History
DepositionJun 8, 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)28,6964
Polymers28,0511
Non-polymers6443
Water7,008389
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 area9510 Å2
Unit cell
Length a, b, c (Å)39.500, 67.929, 40.256
Angle α, β, γ (deg.)90.000, 93.510, 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-XQ5 / 7-[(1~{S})-1-[4-(carbamimidamidomethyl)-1,2,3-triazol-1-yl]ethyl]-3-[3-fluoranyl-4-(methylsulfonylmethyl)phenyl]-1~{H}-indole-2-carboxylic acid


Mass: 513.545 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H24FN7O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 35.99 %
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: 0.976254 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.25→29.04 Å / Num. obs: 56563 / % possible obs: 96.3 % / Redundancy: 6.4 % / Biso Wilson estimate: 11.12 Å2 / CC1/2: 0.999 / Net I/σ(I): 41.1
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.082 / Mean I/σ(I) obs: 13.6 / Num. unique obs: 1961 / CC1/2: 0.991 / Rpim(I) all: 0.042 / Rrim(I) all: 0.092 / % possible all: 67

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→29.04 Å / SU ML: 0.0701 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 10.0527
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1254 5553 5.01 %
Rwork0.1081 105179 -
obs0.1089 55371 95.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.54 Å2
Refinement stepCycle: LAST / Resolution: 1.25→29.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 38 389 2158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00862082
X-RAY DIFFRACTIONf_angle_d1.18122886
X-RAY DIFFRACTIONf_chiral_restr0.0929318
X-RAY DIFFRACTIONf_plane_restr0.0268387
X-RAY DIFFRACTIONf_dihedral_angle_d23.0338344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.260.13971090.1072320X-RAY DIFFRACTION62.12
1.26-1.280.13321380.10072614X-RAY DIFFRACTION71.48
1.28-1.290.15841610.10342867X-RAY DIFFRACTION78.47
1.29-1.310.15591460.10063184X-RAY DIFFRACTION86.16
1.31-1.330.12952100.09523565X-RAY DIFFRACTION98.31
1.33-1.350.11661800.09193635X-RAY DIFFRACTION99.76
1.35-1.360.16471680.08773751X-RAY DIFFRACTION99.95
1.36-1.390.11871790.09063714X-RAY DIFFRACTION99.85
1.39-1.410.13231810.08873664X-RAY DIFFRACTION99.95
1.41-1.430.10022280.09023630X-RAY DIFFRACTION99.87
1.43-1.450.13382010.09123608X-RAY DIFFRACTION99.95
1.45-1.480.11642150.0913673X-RAY DIFFRACTION99.92
1.48-1.510.10671820.0863674X-RAY DIFFRACTION99.82
1.51-1.540.10952010.08353669X-RAY DIFFRACTION99.95
1.54-1.570.11072340.08483631X-RAY DIFFRACTION99.74
1.57-1.610.12491980.08623629X-RAY DIFFRACTION99.66
1.61-1.650.10612280.08723601X-RAY DIFFRACTION99.53
1.65-1.70.12792280.08863591X-RAY DIFFRACTION99.79
1.7-1.750.10671940.08983683X-RAY DIFFRACTION99.61
1.75-1.80.11771890.09293649X-RAY DIFFRACTION99.53
1.8-1.870.12052100.09313627X-RAY DIFFRACTION99.33
1.87-1.940.12371840.09433626X-RAY DIFFRACTION99.06
1.94-2.030.12061710.09393672X-RAY DIFFRACTION98.97
2.03-2.140.11351870.09753607X-RAY DIFFRACTION98.8
2.14-2.270.12342100.10253576X-RAY DIFFRACTION98.03
2.27-2.440.12162150.10473607X-RAY DIFFRACTION98.89
2.44-2.690.12061890.11223619X-RAY DIFFRACTION98.83
2.69-3.080.15871410.12393701X-RAY DIFFRACTION98.49
3.08-3.880.12321670.12573565X-RAY DIFFRACTION97.52
3.88-29.040.15881090.1613227X-RAY DIFFRACTION86.34

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