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- PDB-6zgm: Crystal Structure of the VIM-2 Acquired Metallo-beta-Lactamase in... -

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Basic information

Entry
Database: PDB / ID: 6zgm
TitleCrystal Structure of the VIM-2 Acquired Metallo-beta-Lactamase in Complex with the thiazolecarboxylate inhibitor ANT2681
ComponentsMetallo-beta-lactamase VIM-2-like protein
KeywordsHYDROLASE / Metallo-beta-lactamase / triazole-thione inhibitor / antibiotic resistance / carbapenem-hydrolyzing beta-lactamase
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
ACETATE ION / Chem-QKK / Metallo-beta-lactamase type 2 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsDocquier, J.D. / Pozzi, C. / Marcoccia, F. / De Luca, F. / Benvenuti, M. / Mangani, S.
CitationJournal: Acs Infect Dis. / Year: 2020
Title: ANT2681: SAR Studies Leading to the Identification of a Metallo-beta-lactamase Inhibitor with Potential for Clinical Use in Combination with Meropenem for the Treatment of Infections Caused by ...Title: ANT2681: SAR Studies Leading to the Identification of a Metallo-beta-lactamase Inhibitor with Potential for Clinical Use in Combination with Meropenem for the Treatment of Infections Caused by NDM-ProducingEnterobacteriaceae.
Authors: Davies, D.T. / Leiris, S. / Sprynski, N. / Castandet, J. / Lozano, C. / Bousquet, J. / Zalacain, M. / Vasa, S. / Dasari, P.K. / Pattipati, R. / Vempala, N. / Gujjewar, S. / Godi, S. / ...Authors: Davies, D.T. / Leiris, S. / Sprynski, N. / Castandet, J. / Lozano, C. / Bousquet, J. / Zalacain, M. / Vasa, S. / Dasari, P.K. / Pattipati, R. / Vempala, N. / Gujjewar, S. / Godi, S. / Jallala, R. / Sathyap, R.R. / Darshanoju, N.A. / Ravu, V.R. / Juventhala, R.R. / Pottabathini, N. / Sharma, S. / Pothukanuri, S. / Holden, K. / Warn, P. / Marcoccia, F. / Benvenuti, M. / Pozzi, C. / Mangani, S. / Docquier, J.D. / Lemonnier, M. / Everett, M.
History
DepositionJun 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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: Metallo-beta-lactamase VIM-2-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2897
Polymers25,5391
Non-polymers7506
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-105 kcal/mol
Surface area9840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.960, 78.178, 79.659
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Metallo-beta-lactamase VIM-2-like protein


Mass: 25539.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaVIM / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B8QIQ9, UniProt: Q9K2N0*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-QKK / 5-[[4-(carbamimidamidocarbamoylamino)-3,5-bis(fluoranyl)phenyl]sulfonylamino]-1,3-thiazole-4-carboxylic acid


Mass: 435.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11F2N7O5S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.07 Å3/Da / Density % sol: 40.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M cacodylate, 0.2 M Na-acetate, 5 mM DTT, 26% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→55.8 Å / Num. obs: 25911 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 15.8
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3743 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
SCALA3.3.22data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KO3

1ko3


Resolution: 1.65→51.75 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.44 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY VIM-2 RESIDUES NUMBERED ACCORDING TO THE BBL STANDARD NUMBERING SCH GALLENI ET AL., https://doi.org/10. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY VIM-2 RESIDUES NUMBERED ACCORDING TO THE BBL STANDARD NUMBERING SCH GALLENI ET AL., https://doi.org/10.1128/aac.45.3.660-663.2001 TERMINAL MOIETY OF INHIBITOR ANT2681 POSSIBLY DISORDERED. RESIDUE VAL39 OMITTED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 1209 4.7 %RANDOM
Rwork0.1777 ---
obs0.1799 24701 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.15 Å2 / Biso mean: 27.312 Å2 / Biso min: 7.19 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.65→51.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1749 0 39 171 1959
Biso mean--34.98 38.43 -
Num. residues----233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131853
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171658
X-RAY DIFFRACTIONr_angle_refined_deg1.7741.6572541
X-RAY DIFFRACTIONr_angle_other_deg1.4581.5763839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6645240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.44622.39192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78615266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8541511
X-RAY DIFFRACTIONr_chiral_restr0.0820.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022147
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02390
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 73 -
Rwork0.278 1835 -
all-1908 -
obs--100 %

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