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- PDB-5ni0: VIM-2_10c. Metallo-beta-Lactamase Inhibitors by Bioisosteric Repl... -

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Basic information

Entry
Database: PDB / ID: 5ni0
TitleVIM-2_10c. Metallo-beta-Lactamase Inhibitors by Bioisosteric Replacement: Preparation, Activity and Binding
ComponentsBeta-lactamase class B VIM-2
KeywordsHYDROLASE / inhibition properties / bioisosters / thiols / metallo-beta-lactamase inhibitor
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / periplasmic space / hydrolase activity / response to antibiotic / 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-8XW / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.673 Å
AuthorsSkagseth, S. / Akhter, S. / Paulsen, M.H. / Samuelsen, O. / Muhammad, Z. / Leiros, H.-K.S. / Bayer, A.
CitationJournal: Eur J Med Chem / Year: 2017
Title: Metallo-beta-lactamase inhibitors by bioisosteric replacement: Preparation, activity and binding.
Authors: Skagseth, S. / Akhter, S. / Paulsen, M.H. / Muhammad, Z. / Lauksund, S. / Leiros, H.S. / Bayer, A.
History
DepositionMar 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase class B VIM-2
E: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6008
Polymers56,7062
Non-polymers8946
Water8,251458
1
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8004
Polymers28,3531
Non-polymers4473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8004
Polymers28,3531
Non-polymers4473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.716, 91.070, 122.912
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase class B VIM-2 / BlaVIM-2 / Class B carbapenemase VIM-2 / Metallo beta-lactamase / Metallo-beta lactamase protein / ...BlaVIM-2 / Class B carbapenemase VIM-2 / Metallo beta-lactamase / Metallo-beta lactamase protein / Metallo-beta-lactamase VIM-2 / VIM-2 / VIM-2 beta-lactamase / VIM-2 class B metallo b-lactamase / VIM-2 type metallo-beta-lactamase


Mass: 28352.836 Da / Num. of mol.: 2
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
Production host: Escherichia coli (E. coli) / References: UniProt: Q9K2N0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-8XW / [(2~{R})-1-ethanoylsulfanyl-6-phenyl-hexan-2-yl]phosphonic acid


Mass: 316.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H21O4PS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion / Details: 22-27% PEG 3350, 0.2 M Magnesium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.67→25 Å / Num. obs: 56573 / % possible obs: 94.12 % / Redundancy: 6.4 % / Biso Wilson estimate: 20.49 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.102 / Net I/σ(I): 10.8

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MM9

5mm9


Resolution: 1.673→24.77 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2
RfactorNum. reflection% reflection
Rfree0.214 2780 4.92 %
Rwork0.1778 --
obs0.1797 56544 94.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.673→24.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3457 0 44 458 3959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113618
X-RAY DIFFRACTIONf_angle_d1.3234956
X-RAY DIFFRACTIONf_dihedral_angle_d14.9511293
X-RAY DIFFRACTIONf_chiral_restr0.054567
X-RAY DIFFRACTIONf_plane_restr0.007651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6732-1.70210.3381060.31852470X-RAY DIFFRACTION86
1.7021-1.7330.33521570.29892729X-RAY DIFFRACTION98
1.733-1.76640.28671220.28662762X-RAY DIFFRACTION97
1.7664-1.80240.31971480.27752746X-RAY DIFFRACTION98
1.8024-1.84160.28081350.24492685X-RAY DIFFRACTION95
1.8416-1.88440.26671480.23482731X-RAY DIFFRACTION97
1.8844-1.93150.26191320.23752690X-RAY DIFFRACTION95
1.9315-1.98370.26371460.20532707X-RAY DIFFRACTION95
1.9837-2.04210.22491450.19492676X-RAY DIFFRACTION96
2.0421-2.10790.22131180.19032696X-RAY DIFFRACTION95
2.1079-2.18320.22521500.1762665X-RAY DIFFRACTION93
2.1832-2.27060.23571270.18152694X-RAY DIFFRACTION95
2.2706-2.37380.25031450.17462677X-RAY DIFFRACTION95
2.3738-2.49890.21541420.17052693X-RAY DIFFRACTION95
2.4989-2.65530.20871310.16242707X-RAY DIFFRACTION94
2.6553-2.860.19631380.16712671X-RAY DIFFRACTION92
2.86-3.14730.17141610.16332684X-RAY DIFFRACTION95
3.1473-3.60160.22421570.15142680X-RAY DIFFRACTION93
3.6016-4.5330.1621410.13242658X-RAY DIFFRACTION90
4.533-24.77290.17461310.16442743X-RAY DIFFRACTION89

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