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- PDB-8rii: Structure of E166A BlaC from Mycobacterium tuberculosis at pH 6.5 -

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Basic information

Entry
Database: PDB / ID: 8rii
TitleStructure of E166A BlaC from Mycobacterium tuberculosis at pH 6.5
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / extracellular region / plasma membrane
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
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSun, J. / Bruenle, S. / Ubbink, M.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Scholarship Council China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: A low-barrier proton shared between two aspartates acts as a conformational switch that changes the substrate specificity of the beta-lactamase BlaC.
Authors: Sun, J. / Boyle, A.L. / Brunle, S. / Ubbink, M.
History
DepositionDec 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Structure summary
Category: diffrn_detector / diffrn_source / pdbx_entry_details
Item: _diffrn_detector.type / _diffrn_source.pdbx_synchrotron_beamline ..._diffrn_detector.type / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)28,2151
Polymers28,2151
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.850, 54.680, 80.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 28214.689 Da / Num. of mol.: 1 / Mutation: E166A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: blaC, blaA, Rv2068c, MTCY49.07c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WKD3, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.09 Å3/Da / Density % sol: 41.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MB1 6.5 pH (Buffer) 34.643 %w/v M1K3350 (Precipitant) 0.08 M alcohols (Complex ingredient)

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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: Nov 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 10949 / % possible obs: 99.8 % / Redundancy: 2.3 % / CC1/2: 0.889 / Net I/σ(I): 4.5
Reflection shellResolution: 2.3→2.34 Å / Num. unique obs: 534 / CC1/2: 0.824

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→40 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 37.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3176 508 4.65 %RANDOM
Rwork0.271 ---
obs0.2733 10932 99.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1985 0 0 80 2065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.689
X-RAY DIFFRACTIONf_dihedral_angle_d5.407293
X-RAY DIFFRACTIONf_chiral_restr0.042319
X-RAY DIFFRACTIONf_plane_restr0.005367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.530.41981230.30352543X-RAY DIFFRACTION100
2.53-2.90.37861160.30472584X-RAY DIFFRACTION100
2.9-3.650.30171100.26642613X-RAY DIFFRACTION99
3.65-400.27711590.24972684X-RAY DIFFRACTION99

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