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- PDB-9qi6: Structure of I105R BlaC from Mycobacterium tuberculosis bound to ... -

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Basic information

Entry
Database: PDB / ID: 9qi6
TitleStructure of I105R BlaC from Mycobacterium tuberculosis bound to the trans-enamine adduct of clavulanic acid
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase / BlaC / clavulanic acid
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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 / (2E)-3-[(4-hydroxy-2-oxobutyl)amino]prop-2-enal / DI(HYDROXYETHYL)ETHER / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChikunova, A. / Radojkovic, M. / Ubbink, M.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: To Be Published
Title: High-resolution activity and inhibitor profiling of residue 105 in class A beta-lactamases
Authors: Radojkovic, M. / Koene, S.F. / Chikunova, A. / Timmer, M. / Natarajan, S.V. / Ubbink, M.
History
DepositionMar 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,04519
Polymers56,6342
Non-polymers1,41117
Water7,062392
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,13811
Polymers28,3171
Non-polymers82110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9078
Polymers28,3171
Non-polymers5907
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.495, 41.351, 269.672
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 28316.760 Da / Num. of mol.: 2 / 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, 409 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-ISS / (2E)-3-[(4-hydroxy-2-oxobutyl)amino]prop-2-enal


Mass: 157.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 1.94 Å3/Da / Density % sol: 36.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.46 / Details: 0.067M Zn Chloride, 0.2M Na Acetate, 22%v/v PEGSM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.8→53.93 Å / Num. obs: 42289 / % possible obs: 99.8 % / Redundancy: 5.5 % / CC1/2: 0.994 / Net I/σ(I): 8.6
Reflection shellResolution: 1.8→1.84 Å / Num. unique obs: 2409 / CC1/2: 0.72

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→44.99 Å / SU B: 3.712 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.133 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21731 2002 4.7 %RANDOM
Rwork0.18647 ---
obs0.18797 40184 99.74 %-
Displacement parametersBiso mean: 21.507 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å2-0 Å20 Å2
2--1.97 Å2-0 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3984 0 78 392 4454

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