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- PDB-5lcf: VIM-2 metallo-beta-lactamase in complex with 3-oxo-2-phenylisoind... -

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Basic information

Entry
Database: PDB / ID: 5lcf
TitleVIM-2 metallo-beta-lactamase in complex with 3-oxo-2-phenylisoindoline-4-carboxylic acid (compound 30)
ComponentsMetallo-beta-lactamase VIM-2
KeywordsHYDROLASE / metallo-beta-lactamase / inhibitor / complex / antibiotic resistance
Function / homology
Function and homology information


beta-lactamase / hydrolase activity / metal ion binding
Similarity search - Function
: / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6TJ / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 Å
AuthorsLi, G.-B. / Brem, J. / McDonough, M.A. / Schofield, C.J.
CitationJournal: Chem Sci / Year: 2017
Title: NMR-filtered virtual screening leads to non-metal chelating metallo-beta-lactamase inhibitors.
Authors: Li, G.B. / Abboud, M.I. / Brem, J. / Someya, H. / Lohans, C.T. / Yang, S.Y. / Spencer, J. / Wareham, D.W. / McDonough, M.A. / Schofield, C.J.
History
DepositionJun 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metallo-beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9457
Polymers28,3531
Non-polymers5936
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-83 kcal/mol
Surface area9010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.460, 65.637, 70.721
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Metallo-beta-lactamase VIM-2 / Beta-lactamase / Beta-lactamase VIM-2 / Class B carbapenemase VIM-2 / Metallo beta lactamase VIM-2 ...Beta-lactamase / Beta-lactamase VIM-2 / Class B carbapenemase VIM-2 / Metallo beta lactamase VIM-2 / Metallo beta-lactamase / Metallo-beta-lactamase / Metallo-beta-lactamase vim-2 / VIM-2 metallo-beta-lactamase / VIM-2 protein


Mass: 28352.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, blm, VIM-2, vim-2, PAERUG_P32_London_17_VIM_2_10_11_06255
Plasmid: OPINF / Details (production host): PLASMID DERIVED NON-GENOMIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold pLysS AG / References: UniProt: Q9K2N0

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Non-polymers , 5 types, 253 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-6TJ / 3-oxidanylidene-2-phenyl-1~{H}-isoindole-4-carboxylic acid


Mass: 253.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11NO3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O

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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: 1.83 Å3/Da / Density % sol: 32.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Magnesium Formate, 21% (v/v) Polyethylene glycol 3350, 5 mM 3-oxo-2-phenylisoindoline-4-carboxylic acid, 16 mg/mL protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.542 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 13, 2016 / Details: OSMIC HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 16377 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 14.94 Å2 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.024 / Rrim(I) all: 0.062 / Χ2: 1.06 / Net I/av σ(I): 26.418 / Net I/σ(I): 18.2 / Num. measured all: 110191
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.86-1.935.70.163197.9
1.93-26.80.135199.9
2-2.096.90.113199.6
2.09-2.216.90.1199.8
2.21-2.346.90.088199.9
2.34-2.526.90.0781100
2.52-2.786.90.0661100
2.78-3.186.90.0541100
3.18-4.016.90.0431100
4.01-506.50.034198.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.8 Å24.05 Å
Translation5.8 Å24.05 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.6.0phasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
CrystalCleardata reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C1D

4c1d


Resolution: 1.86→24.055 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.06
RfactorNum. reflection% reflection
Rfree0.1642 1623 9.94 %
Rwork0.1266 --
obs0.1303 16334 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 52.86 Å2 / Biso mean: 15.2723 Å2 / Biso min: 5.02 Å2
Refinement stepCycle: final / Resolution: 1.86→24.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1653 0 34 249 1936
Biso mean--23.83 27.55 -
Num. residues----222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011751
X-RAY DIFFRACTIONf_angle_d0.7712378
X-RAY DIFFRACTIONf_chiral_restr0.052268
X-RAY DIFFRACTIONf_plane_restr0.005312
X-RAY DIFFRACTIONf_dihedral_angle_d12.6671000
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8601-1.91480.19841310.1551171130298
1.9148-1.97660.16221270.13051201132899
1.9766-2.04720.1861230.112112141337100
2.0472-2.12910.15761450.110112041349100
2.1291-2.2260.16481370.116711981335100
2.226-2.34320.17281280.118712291357100
2.3432-2.48990.18711340.116112101344100
2.4899-2.68190.15811400.123512311371100
2.6819-2.95140.15911390.13312201359100
2.9514-3.37740.15891400.121112521392100
3.3774-4.25140.1371310.117112521383100
4.2514-24.05670.17471480.152513291477100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.92280.756-0.0732.59990.34762.53940.02530.0750.068-0.19770.0125-0.005-0.06720.0795-0.03330.07160.02030.01010.07470.00720.0317-36.51783.76667.3047
20.81920.08040.245.50595.54475.615-0.03090.09430.0986-0.290.0142-0.0393-0.2738-0.12660.01130.10060.0142-0.0070.09970.0350.0704-43.467385.76721.6057
31.82750.04760.27440.79770.08660.99220.0289-0.1636-0.05480.0661-0.0198-0.02370.0546-0.0009-0.00440.08430.00250.00470.07080.0120.0536-34.532579.763620.0582
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 40 through 88 )A40 - 88
2X-RAY DIFFRACTION2chain 'A' and (resid 89 through 102 )A89 - 102
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 260 )A103 - 260

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