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- PDB-6mkq: Carbapenemase VCC-1 bound to avibactam -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6mkq
TitleCarbapenemase VCC-1 bound to avibactam
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / carbapenemase / VCC-1 / avibactam / beta-lactamase / Vibrio cholerae / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NXL / beta-lactamase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMark, B.L. / Vadlamani, G.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)148496 Canada
CitationJournal: Antimicrob. Agents Chemother. / Year: 2019
Title: Molecular Basis for the Potent Inhibition of the Emerging Carbapenemase VCC-1 by Avibactam.
Authors: Mangat, C.S. / Vadlamani, G. / Holicek, V. / Chu, M. / Larmour, V.L.C. / Vocadlo, D.J. / Mulvey, M.R. / Mark, B.L.
History
DepositionSep 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4972
Polymers29,2301
Non-polymers2671
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.060, 62.060, 134.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-475-

HOH

21A-588-

HOH

31A-634-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 29229.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U3IB62, beta-lactamase
#2: Chemical ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form


Mass: 267.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C7H13N3O6S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic, inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.7 M NaCl, 0.2 M Bis-Tris pH 5.5 and 22% PEG 3350, 5% (w/v) glycerol, 10 mg/ml Vcc-1. Then soaked with 1 mM avibactam for 24 hrs

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→56.34 Å / Num. obs: 21085 / % possible obs: 98 % / Redundancy: 5.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.126 / Net I/σ(I): 9.3
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.636 / Num. unique all: 1236 / CC1/2: 0.827

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MK6, chain D

6mk6


Resolution: 1.9→41.714 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.45
RfactorNum. reflection% reflection
Rfree0.1967 1999 9.51 %
Rwork0.1573 --
obs0.1611 21019 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→41.714 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 17 248 2278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072070
X-RAY DIFFRACTIONf_angle_d0.8722802
X-RAY DIFFRACTIONf_dihedral_angle_d3.3391239
X-RAY DIFFRACTIONf_chiral_restr0.046306
X-RAY DIFFRACTIONf_plane_restr0.005368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.29941310.22251243X-RAY DIFFRACTION90
1.9475-2.00020.23591320.19051250X-RAY DIFFRACTION93
2.0002-2.0590.21491340.17231277X-RAY DIFFRACTION95
2.059-2.12550.22241360.16681307X-RAY DIFFRACTION96
2.1255-2.20150.24511390.15741324X-RAY DIFFRACTION98
2.2015-2.28960.20851420.1481355X-RAY DIFFRACTION99
2.2896-2.39380.19811450.14881373X-RAY DIFFRACTION100
2.3938-2.520.18821430.14221360X-RAY DIFFRACTION100
2.52-2.67790.17691460.14611387X-RAY DIFFRACTION100
2.6779-2.88460.19251440.14161376X-RAY DIFFRACTION100
2.8846-3.17480.19321470.15641399X-RAY DIFFRACTION100
3.1748-3.63390.17721500.13611417X-RAY DIFFRACTION100
3.6339-4.57740.15481490.13431418X-RAY DIFFRACTION99
4.5774-41.72420.21921610.20051534X-RAY DIFFRACTION100

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