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- PDB-9hit: Structure of P167S/D240G BlaC from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 9hit
TitleStructure of P167S/D240G BlaC from Mycobacterium tuberculosis
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
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
CITRIC ACID / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSun, J. / Bruenle, S. / Ubbink, M.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Protein Sci. / Year: 2025
Title: Directed evolution of a beta-lactamase samples a wide variety of conformational states.
Authors: Sun, J. / Timmer, M. / Brunle, S. / Boyle, A.L. / Ubbink, M.
History
DepositionNov 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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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)28,4682
Polymers28,2761
Non-polymers1921
Water4,756264
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint0 kcal/mol
Surface area10880 Å2
Unit cell
Length a, b, c (Å)38.899, 54.448, 53.943
Angle α, β, γ (deg.)90.00, 92.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 28275.727 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.02 Å3/Da / Density % sol: 39.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium cacodylate pH 6.07 1.16 M trisodium citrate (Precipitant)

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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: Sep 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→38.9 Å / Num. obs: 55085 / % possible obs: 99.5 % / Redundancy: 1.3 % / CC1/2: 0.995 / Net I/σ(I): 7.2
Reflection shellResolution: 1.3→1.32 Å / Num. unique obs: 2733 / CC1/2: 0.548

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Processing

Software
NameVersionClassification
REFMAC1refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→38.9 Å / SU B: 2.001 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.046 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.179 2565 4.7 %RANDOM
Rwork0.1412 ---
obs0.154 55067 99.47 %-
Displacement parametersBiso mean: 7.946 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0 Å2-0.36 Å2
2---0.39 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.3→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1989 0 13 264 2266

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