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- PDB-6zyo: Structure of VIM-2 with 2-Mercaptomethyl-thiazolidine D-syn-1b -

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Basic information

Entry
Database: PDB / ID: 6zyo
TitleStructure of VIM-2 with 2-Mercaptomethyl-thiazolidine D-syn-1b
ComponentsBeta-lactamase VIM-2
KeywordsANTIMICROBIAL PROTEIN / metallo-b-lactamase / inhibitor / antiboitic resistance
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
FORMIC ACID / Chem-QST / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsHinchliffe, P. / Spencer, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Chem Sci / Year: 2021
Title: 2-Mercaptomethyl-thiazolidines use conserved aromatic-S interactions to achieve broad-range inhibition of metallo-beta-lactamases.
Authors: Rossi, M.A. / Martinez, V. / Hinchliffe, P. / Mojica, M.F. / Castillo, V. / Moreno, D.M. / Smith, R. / Spellberg, B. / Drusano, G.L. / Banchio, C. / Bonomo, R.A. / Spencer, J. / Vila, A.J. / Mahler, G.
History
DepositionAug 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,52214
Polymers51,3872
Non-polymers1,13512
Water7,963442
1
A: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2617
Polymers25,6931
Non-polymers5686
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2617
Polymers25,6931
Non-polymers5686
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.530, 79.740, 68.040
Angle α, β, γ (deg.)90.000, 130.500, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-564-

HOH

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Components

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


Mass: 25693.488 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 BL21(DE3) (bacteria) / References: UniProt: Q9K2N0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-QST / (2~{S},4~{S})-2-ethoxycarbonyl-5,5-dimethyl-2-(sulfanylmethyl)-1,3-thiazolidine-4-carboxylic acid


Mass: 279.376 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17NO4S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.08 Å3/Da / Density % sol: 40.81 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.2 M MAGNESIUM FORMATE, 20 % W/V PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.45→51.76 Å / Num. obs: 73396 / % possible obs: 98.7 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rpim(I) all: 0.027 / Net I/σ(I): 16.8
Reflection shellResolution: 1.45→1.48 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3591 / CC1/2: 0.675 / Rpim(I) all: 0.497

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZ3

4bz3


Resolution: 1.45→51.757 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1633 3522 4.8 %
Rwork0.1242 69867 -
obs0.1262 73389 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.29 Å2 / Biso mean: 24.8383 Å2 / Biso min: 11.27 Å2
Refinement stepCycle: final / Resolution: 1.45→51.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 92 442 4020
Biso mean--31.16 37.8 -
Num. residues----464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093787
X-RAY DIFFRACTIONf_angle_d0.9865217
X-RAY DIFFRACTIONf_chiral_restr0.082589
X-RAY DIFFRACTIONf_plane_restr0.008693
X-RAY DIFFRACTIONf_dihedral_angle_d13.9081337
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.45-1.46990.32311370.2829273498
1.4699-1.49090.29091240.2496276498
1.4909-1.51310.27091190.2069281098
1.5131-1.53680.27981210.1737275298
1.5368-1.5620.21711270.1506277998
1.562-1.58890.18461310.1402279798
1.5889-1.61780.23011370.1349274198
1.6178-1.64890.19021560.1307277598
1.6489-1.68260.20361260.1286280399
1.6826-1.71920.17271250.1225283098
1.7192-1.75920.17831760.1112271499
1.7592-1.80320.14911490.1094276699
1.8032-1.85190.14921770.1047273199
1.8519-1.90640.17171200.0999285499
1.9064-1.9680.1691520.1016277199
1.968-2.03830.13831480.1005280999
2.0383-2.11990.15051590.0987278699
2.1199-2.21640.15021120.1081280099
2.2164-2.33320.13691410.1105285199
2.3332-2.47940.14461250.107281199
2.4794-2.67090.15641230.1199284199
2.6709-2.93960.16521480.12312834100
2.9396-3.36490.15331330.12322823100
3.3649-4.23910.14821740.1179281399
4.2391-51.750.16611820.15062878100

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