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- PDB-5nhz: VIM-2_10b. Metallo-beta-Lactamase Inhibitors by Bioisosteric Repl... -

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Basic information

Entry
Database: PDB / ID: 5nhz
TitleVIM-2_10b. 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 / hydrolase activity / metal ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8XZ / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSkagseth, S. / Akhter, S. / Paulsen, M.H. / Samuelsen, O. / Muhammad, Z. / Leiros, K.-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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_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_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 / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,18416
Polymers56,7062
Non-polymers1,47914
Water5,891327
1
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0117
Polymers28,3531
Non-polymers6596
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-28 kcal/mol
Surface area9480 Å2
MethodPISA
2
B: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1739
Polymers28,3531
Non-polymers8208
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-52 kcal/mol
Surface area9530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.779, 90.872, 124.075
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 8 types, 341 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-8XZ / [(2~{R})-1-ethanoylsulfanyl-5-phenyl-pentan-2-yl]phosphonic acid


Mass: 302.326 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19O4PS
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.28 Å3/Da / Density % sol: 45.95 %
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 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.85→25 Å / Num. obs: 45000 / % possible obs: 99.93 % / Redundancy: 6.5 % / Biso Wilson estimate: 27.24 Å2 / Net I/σ(I): 14.6

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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: 1.85→24.754 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 18.75
RfactorNum. reflection% reflection
Rfree0.2039 2206 4.9 %
Rwork0.1662 --
obs0.168 44986 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→24.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 72 327 3865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113660
X-RAY DIFFRACTIONf_angle_d1.3155014
X-RAY DIFFRACTIONf_dihedral_angle_d15.7511287
X-RAY DIFFRACTIONf_chiral_restr0.06568
X-RAY DIFFRACTIONf_plane_restr0.007658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.89020.2511310.24062633X-RAY DIFFRACTION100
1.8902-1.93420.26261560.22862592X-RAY DIFFRACTION100
1.9342-1.98250.23121370.20762659X-RAY DIFFRACTION100
1.9825-2.03610.21411360.19752622X-RAY DIFFRACTION100
2.0361-2.0960.24821360.1932633X-RAY DIFFRACTION100
2.096-2.16360.21111320.17612657X-RAY DIFFRACTION100
2.1636-2.24090.23021250.16672639X-RAY DIFFRACTION100
2.2409-2.33060.20581430.16132667X-RAY DIFFRACTION100
2.3306-2.43650.18931310.15532663X-RAY DIFFRACTION100
2.4365-2.56490.20061370.15642663X-RAY DIFFRACTION100
2.5649-2.72540.19221240.15942672X-RAY DIFFRACTION100
2.7254-2.93550.23191310.16482699X-RAY DIFFRACTION100
2.9355-3.23030.18851340.15612697X-RAY DIFFRACTION100
3.2303-3.69640.16881670.14172669X-RAY DIFFRACTION100
3.6964-4.65210.18221330.1422763X-RAY DIFFRACTION100
4.6521-24.75580.22731530.18892852X-RAY DIFFRACTION99
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)
14.11743.25070.78037.22931.28711.7472-0.0445-0.1759-0.3331-0.17110.0475-0.35530.12370.0799-0.00820.16430.01950.01530.17410.06570.1737-2.279111.4824-8.3721
22.2091-0.115-0.59281.56970.06154.17880.02210.25430.1455-0.3837-0.0446-0.12860.02420.10730.02020.2278-0.01010.01140.20680.05880.2363-2.530719.5575-17.9937
35.52672.35525.16312.2572.07914.9513-0.00320.5874-0.6923-0.68410.0898-0.1770.53330.6838-0.23220.62120.06780.07640.4555-0.01780.41111.4866.5385-31.3483
47.35071.73624.4696.2226-2.68916.2212-0.1635-0.68490.54120.27270.1130.1119-0.4466-0.42150.05490.2550.02570.01780.2166-0.0690.2796-19.3538-2.7476-6.0904
56.65384.4007-1.75637.4912-1.79852.4211-0.18620.06970.0042-0.31270.2150.1035-0.0104-0.1092-0.04630.16370.015-0.0210.14260.00580.1199-22.104-13.5018-8.5348
65.095-4.0498-3.00016.36621.78392.95310.143-0.72970.13110.3275-0.07570.0394-0.2099-0.1399-0.1950.1567-0.0002-0.00630.25010.01860.1823-17.5878-14.67060.1497
73.01580.45860.9412.457-0.20424.0417-0.11470.5773-0.4733-0.58060.118-0.06770.2206-0.0113-0.00730.3004-0.03360.01660.2522-0.09380.3055-20.6163-23.3945-16.7978
85.0197-0.5295-1.63223.7923.29343.1898-0.28631.15320.6417-1.49870.2444-0.6398-1.2181.0119-0.00820.9671-0.2205-0.03210.82750.14640.4203-19.752-6.7274-25.4227
97.30390.1905-6.2344.8233-1.08048.369-0.12670.8467-0.3341-0.7548-0.32850.6892-0.35950.02190.35980.648-0.0164-0.19020.6891-0.12850.3802-29.2751-15.9674-30.6526
107.4685-3.37030.1259.2883-0.56358.1577-0.48150.14460.2022-0.16460.33661.1272-0.3978-0.71460.21490.37040.0677-0.06180.37550.03450.3152-32.1329-10.8791-17.4081
111.6971-1.5707-0.04356.7098-2.93411.72240.05671.14850.4229-1.0785-0.05130.0255-0.8488-0.36530.2580.9025-0.1306-0.1560.72460.07830.3628-26.82-5.2619-30.2395
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 88 )
2X-RAY DIFFRACTION2chain 'A' and (resid 89 through 279 )
3X-RAY DIFFRACTION3chain 'A' and (resid 280 through 295 )
4X-RAY DIFFRACTION4chain 'B' and (resid 30 through 42 )
5X-RAY DIFFRACTION5chain 'B' and (resid 43 through 88 )
6X-RAY DIFFRACTION6chain 'B' and (resid 89 through 103 )
7X-RAY DIFFRACTION7chain 'B' and (resid 104 through 222 )
8X-RAY DIFFRACTION8chain 'B' and (resid 223 through 238 )
9X-RAY DIFFRACTION9chain 'B' and (resid 239 through 252 )
10X-RAY DIFFRACTION10chain 'B' and (resid 253 through 279 )
11X-RAY DIFFRACTION11chain 'B' and (resid 280 through 295 )

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