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- PDB-6kw1: The structure of the metallo-beta-lactamase VIM-2 in complex with... -

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Basic information

Entry
Database: PDB / ID: 6kw1
TitleThe structure of the metallo-beta-lactamase VIM-2 in complex with a triazolylthioacetamide 1b
ComponentsBeta-lactamase class B VIM-2
KeywordsHYDROLASE / Antibiotic resistant / Metallo-beta-lactamase VIM-2 inhibitor / Trizolylthioacetamides / Crystallographic study
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
Chem-9RX / ACETATE ION / FORMIC ACID / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77521201035 Å
AuthorsYang, K.W. / Xiang, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China81361138018 China
National Natural Science Foundation of China21572179 China
CitationJournal: Biomolecules / Year: 2020
Title: Kinetic, Thermodynamic, and Crystallographic Studies of 2-Triazolylthioacetamides as Verona Integron-Encoded Metallo-beta-Lactamase 2 (VIM-2) Inhibitor.
Authors: Xiang, Y. / Zhang, Y.J. / Ge, Y. / Zhou, Y. / Chen, C. / Wahlgren, W.Y. / Tan, X. / Chen, X. / Yang, K.W.
History
DepositionSep 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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 class B VIM-2
B: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,24922
Polymers56,7062
Non-polymers1,54320
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-111 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.759, 79.421, 67.981
Angle α, β, γ (deg.)90.000, 130.938, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-lactamase class B VIM-2 / Beta-lactamase / BlaVIM-2 / Metallo beta-lactamase / Metallo-beta-lactamase VIM-2 / Subclass B1 ...Beta-lactamase / BlaVIM-2 / Metallo beta-lactamase / Metallo-beta-lactamase VIM-2 / Subclass B1 metallo-beta-lactamase VIM-2 / VIM-2 / VIM-2 class B metallo b-lactamase / VIM-2 metallo-beta-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, VIM-2, vim-2, IPC669_36195
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K2N0

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Non-polymers , 8 types, 344 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-9RX / 2-[3-[2-(1H-benzimidazol-2-ylamino)-2-oxidanylidene-ethyl]sulfanyl-1H-1,2,4-triazol-5-yl]benzoic acid


Mass: 394.407 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H14N6O3S
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.87 Å3/Da / Density % sol: 34.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 8000, 0.1M MES, pH 6.5, 0.1M magnesium acetate

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Data collection

DiffractionMean temperature: 97 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.775→39.1907632483 Å / Num. obs: 39958 / % possible obs: 99.13 % / Redundancy: 10 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.055 / Net I/σ(I): 6.38
Reflection shellResolution: 1.775→1.839 Å / Num. unique obs: 39958 / Rrim(I) all: 0.14 / % possible all: 99.13

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Blu-Icedata collection
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ko3

1ko3


Resolution: 1.77521201035→39.1907632483 Å / SU ML: 0.164202998798 / Cross valid method: FREE R-VALUE / σ(F): 1.38229043876 / Phase error: 21.0323134189
RfactorNum. reflection% reflection
Rfree0.206324845679 2019 5.05407029138 %
Rwork0.176544854667 --
obs0.178080634821 39948 99.1388509741 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.9373964541 Å2
Refinement stepCycle: LAST / Resolution: 1.77521201035→39.1907632483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 84 324 3894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00392522518413640
X-RAY DIFFRACTIONf_angle_d0.6856642335734976
X-RAY DIFFRACTIONf_chiral_restr0.0495713551409560
X-RAY DIFFRACTIONf_plane_restr0.00398587243297654
X-RAY DIFFRACTIONf_dihedral_angle_d13.31346546222098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77521201035-1.81960.2221154888541300.1919431486352457X-RAY DIFFRACTION90.1707912165
1.8196-1.86880.2345370891511490.1865329677772747X-RAY DIFFRACTION99.9654815326
1.8688-1.92380.2420431139271450.1797716661452706X-RAY DIFFRACTION100
1.9238-1.98590.2191308852411380.1827213741612715X-RAY DIFFRACTION99.8599929996
1.9859-2.05690.2251877035871430.1709630555052687X-RAY DIFFRACTION99.4378074491
2.0569-2.13920.1809313933521430.1735654343342724X-RAY DIFFRACTION100
2.1392-2.23660.1931587875571460.1733467698792730X-RAY DIFFRACTION99.9652415711
2.2366-2.35450.2260451439731330.1858769131482725X-RAY DIFFRACTION99.9300699301
2.3545-2.50190.2352994658921520.1804898907452729X-RAY DIFFRACTION99.7921718046
2.5019-2.69510.2169367757971520.1815134462782724X-RAY DIFFRACTION99.9305072967
2.6951-2.96620.2390476718261450.17405218022741X-RAY DIFFRACTION100
2.9662-3.39520.1838159917951470.1694667157842720X-RAY DIFFRACTION99.7911590672
3.3952-4.27680.18183530431480.1602030125432750X-RAY DIFFRACTION99.8277643817
4.2768-39.19070.1938333159051480.188100977582774X-RAY DIFFRACTION99.3201903467
Refinement TLS params.

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

ID