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- PDB-6mk6: Carbapenemase VCC-1 from Vibrio cholerae N14-02106 -

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Basic information

Entry
Database: PDB / ID: 6mk6
TitleCarbapenemase VCC-1 from Vibrio cholerae N14-02106
ComponentsBeta-lactamase
KeywordsHYDROLASE / Carbapenemase / VCC-1 / Vibrio cholerae N14-02106 / beta-lactamase
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
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 25, 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 / 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

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
D: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)116,9204
Polymers116,9204
Non-polymers00
Water24,1581341
1
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)29,2301
Polymers29,2301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)29,2301
Polymers29,2301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)29,2301
Polymers29,2301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)29,2301
Polymers29,2301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Beta-lactamase
C: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)58,4602
Polymers58,4602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-11 kcal/mol
Surface area20260 Å2
MethodPISA
6
B: Beta-lactamase
D: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)58,4602
Polymers58,4602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-11 kcal/mol
Surface area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.930, 46.650, 113.610
Angle α, β, γ (deg.)90.00, 99.28, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-361-

HOH

21B-465-

HOH

31B-618-

HOH

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Components

#1: Protein
Beta-lactamase /


Mass: 29229.900 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1341 / 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: 2.35 Å3/Da / Density % sol: 47.61 %
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 and 12-18 mg/mL VCC-1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→56.06 Å / Num. obs: 119395 / % possible obs: 99.5 % / Redundancy: 4.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Net I/σ(I): 13.8
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.303 / Num. unique all: 5879 / CC1/2: 0.97

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Processing

Software
NameVersionClassification
PHENIX(1.13rc2_2986: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BUE

1bue


Resolution: 1.7→51.796 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.93
RfactorNum. reflection% reflection
Rfree0.2011 1466 1.23 %
Rwork0.1641 --
obs0.1645 119330 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→51.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8026 0 0 1341 9367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098182
X-RAY DIFFRACTIONf_angle_d0.97411059
X-RAY DIFFRACTIONf_dihedral_angle_d10.3984937
X-RAY DIFFRACTIONf_chiral_restr0.0561210
X-RAY DIFFRACTIONf_plane_restr0.0061451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.76080.24851430.205611562X-RAY DIFFRACTION99
1.7608-1.83130.23611460.197611644X-RAY DIFFRACTION99
1.8313-1.91460.22491440.194911677X-RAY DIFFRACTION99
1.9146-2.01560.23321460.185211673X-RAY DIFFRACTION99
2.0156-2.14190.20451460.17911740X-RAY DIFFRACTION99
2.1419-2.30720.21261470.169311742X-RAY DIFFRACTION99
2.3072-2.53940.23761460.168311810X-RAY DIFFRACTION100
2.5394-2.90690.20411480.1611905X-RAY DIFFRACTION100
2.9069-3.66220.19311490.153411934X-RAY DIFFRACTION100
3.6622-51.81960.16911510.148712177X-RAY DIFFRACTION99

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