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- PDB-8ph3: Crystal structure of the metallo-beta-lactamase VIM1 with 3747 -

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Basic information

Entry
Database: PDB / ID: 8ph3
TitleCrystal structure of the metallo-beta-lactamase VIM1 with 3747
ComponentsBeta-lactamase VIM-1
KeywordsANTIMICROBIAL PROTEIN / Complex / metallo-beta-lactamase / inhibitor / zinc / indole carboxylate
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / hydrolase activity / 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
: / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 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 3747
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,6064
Polymers28,0511
Non-polymers5543
Water6,666370
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 area9500 Å2
Unit cell
Length a, b, c (Å)39.510, 67.810, 40.290
Angle α, β, γ (deg.)90.000, 93.690, 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 (E. coli) / Strain (production host): Q9XAY4 / 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-YQR / 7-[(1~{S})-1-[2-(aminomethyl)-6-oxidanylidene-5-oxa-7-azaspiro[3.4]octan-7-yl]ethyl]-3-(1-methylpyrazol-4-yl)-1~{H}-indole-2-carboxylic acid


Mass: 423.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H25N5O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 35.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging 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: 0.81532 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81532 Å / Relative weight: 1
ReflectionResolution: 1.09→39.43 Å / Num. obs: 85244 / % possible obs: 96.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 12.03 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.018 / Rrim(I) all: 0.045 / Net I/σ(I): 16.3
Reflection shellResolution: 1.09→1.12 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 6121 / CC1/2: 0.845 / Rpim(I) all: 0.267 / Rrim(I) all: 0.688 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.09→34.09 Å / SU ML: 0.0848 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 12.0986
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1481 4251 4.99 %
Rwork0.1254 80959 -
obs0.1265 85210 96.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.85 Å2
Refinement stepCycle: LAST / Resolution: 1.09→34.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 33 370 2134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01242059
X-RAY DIFFRACTIONf_angle_d1.34672855
X-RAY DIFFRACTIONf_chiral_restr0.1032318
X-RAY DIFFRACTIONf_plane_restr0.0139389
X-RAY DIFFRACTIONf_dihedral_angle_d13.3212319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.09-1.10.22331620.19392593X-RAY DIFFRACTION95.03
1.1-1.120.19661510.1712582X-RAY DIFFRACTION93.72
1.12-1.130.20451410.16742650X-RAY DIFFRACTION94.8
1.13-1.140.16781540.14652632X-RAY DIFFRACTION94.86
1.14-1.160.18691510.1382623X-RAY DIFFRACTION94.58
1.16-1.170.15611870.13482547X-RAY DIFFRACTION95.23
1.17-1.190.14511540.12792673X-RAY DIFFRACTION94.96
1.19-1.210.13881390.11932671X-RAY DIFFRACTION95.55
1.21-1.230.13911110.11982693X-RAY DIFFRACTION95.5
1.23-1.250.14541040.1162655X-RAY DIFFRACTION95.67
1.25-1.270.14791490.12092704X-RAY DIFFRACTION96.06
1.27-1.290.18781270.11982645X-RAY DIFFRACTION95.75
1.29-1.320.1241420.11252700X-RAY DIFFRACTION96.5
1.32-1.340.14271570.11042633X-RAY DIFFRACTION95.61
1.34-1.370.13211650.10422685X-RAY DIFFRACTION97.17
1.37-1.410.14631520.09912705X-RAY DIFFRACTION96.91
1.41-1.440.15561180.0982706X-RAY DIFFRACTION96.15
1.44-1.480.13811610.09792695X-RAY DIFFRACTION97.54
1.48-1.520.13421310.09812741X-RAY DIFFRACTION97.65
1.52-1.570.11851210.09732752X-RAY DIFFRACTION97.16
1.57-1.630.12551510.10262664X-RAY DIFFRACTION97.3
1.63-1.690.14551230.10262750X-RAY DIFFRACTION97.65
1.69-1.770.13931180.10412779X-RAY DIFFRACTION98.14
1.77-1.860.12371400.10472753X-RAY DIFFRACTION98.33
1.86-1.980.11351290.10872779X-RAY DIFFRACTION98.48
1.98-2.130.13181880.11182704X-RAY DIFFRACTION98.23
2.13-2.350.13591320.11422790X-RAY DIFFRACTION99.08
2.35-2.690.12831350.12612765X-RAY DIFFRACTION98.01
2.69-3.390.16471300.13982821X-RAY DIFFRACTION99.46
3.39-34.090.1841280.16112869X-RAY DIFFRACTION99.5

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