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- PDB-9hck: Structure of P167S/D240G/D172A/S104G BlaC from Mycobacterium tube... -

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Basic information

Entry
Database: PDB / ID: 9hck
TitleStructure of P167S/D240G/D172A/S104G BlaC from Mycobacterium tuberculosis at pH 5.5
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
AMMONIUM ION / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSun, J. / Bruenle, S. / Ubbink, M.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Scholarship Council 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 10, 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)28,5517
Polymers28,1311
Non-polymers4206
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-37 kcal/mol
Surface area11150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.875, 54.642, 54.163
Angle α, β, γ (deg.)90.00, 93.17, 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: 28130.615 Da / Num. of mol.: 1
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: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.07 Å3/Da / Density % sol: 40.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris buffer, pH 5.5 2 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.6→38.44 Å / Num. obs: 20155 / % possible obs: 95.3 % / Redundancy: 1.6 % / CC1/2: 0.998 / Net I/σ(I): 14.7
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 20155 / CC1/2: 0.861

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→38.44 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.95 / Phase error: 24.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1881 1076 5.35 %
Rwork0.1518 --
obs0.1538 20124 67.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→38.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1955 0 22 291 2268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.787
X-RAY DIFFRACTIONf_dihedral_angle_d13.573718
X-RAY DIFFRACTIONf_chiral_restr0.051316
X-RAY DIFFRACTIONf_plane_restr0.008363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.670.2604170.221439X-RAY DIFFRACTION12
1.67-1.760.2517420.2203995X-RAY DIFFRACTION28
1.76-1.870.2404890.20631600X-RAY DIFFRACTION46
1.87-2.020.21021110.18032272X-RAY DIFFRACTION64
2.02-2.220.20162160.15843147X-RAY DIFFRACTION91
2.22-2.540.19512050.15523493X-RAY DIFFRACTION99
2.54-3.20.20652240.15543511X-RAY DIFFRACTION99
3.2-38.440.1531720.13383591X-RAY DIFFRACTION99

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