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- PDB-9qi7: Crystal structure of I105R mutant of BlaC from Mycobacterium tube... -

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Basic information

Entry
Database: PDB / ID: 9qi7
TitleCrystal structure of I105R mutant of BlaC from Mycobacterium tuberculosis in complex with avibactam
ComponentsBeta-lactamase
KeywordsHYDROLASE / Beta-lactamase / BlaC
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / extracellular region
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
ACETATE ION / Chem-NXL / DI(HYDROXYETHYL)ETHER / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChikunova, A. / Radojkovic, M. / Ubbink, M.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: J.Biol.Chem. / Year: 2025
Title: A glycine at position 105 leads to clavulanic acid and avibactam resistance in class A beta-lactamases.
Authors: Radojkovic, M. / Chikunova, A. / Koene, S.F. / Timmer, M. / Natarajan, S.V. / Boyle, A.L. / Ubbink, M.
History
DepositionMar 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 23, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9168
Polymers28,2021
Non-polymers7147
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-44 kcal/mol
Surface area10960 Å2
Unit cell
Length a, b, c (Å)110.660, 117.068, 51.061
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-306-

ZN

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase / Ambler class A beta-lactamase


Mass: 28201.674 Da / Num. of mol.: 1 / Mutation: I105R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: blaC, blaA, BQ2027_MB2094C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A5I7, beta-lactamase

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Non-polymers , 6 types, 41 molecules

#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: obtained synthetically / Formula: C7H13N3O6S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.93 Å3/Da / Density % sol: 58.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.74 / Details: 0.2M Na Acetate, 22%w/v PEGSM, 0.06M Zn Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.2→80.42 Å / Num. obs: 17265 / % possible obs: 99.9 % / Redundancy: 9.2 % / CC1/2: 0.998 / Net I/σ(I): 12.3
Reflection shellResolution: 2.2→2.27 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1465 / CC1/2: 0.453

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→58.6 Å / SU B: 15.346 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.2 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24107 1748 10.1 %RANDOM
Rwork0.18714 ---
obs0.19237 15496 99.84 %-
Displacement parametersBiso mean: 31.261 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å20 Å2-0 Å2
2--2.13 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.2→58.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 0 40 34 2058

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