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- PDB-9hj2: Structure of P167S/D240G/D172A/S104G/H184R BlaC from Mycobacteriu... -

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Basic information

Entry
Database: PDB / ID: 9hj2
TitleStructure of P167S/D240G/D172A/S104G/H184R 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 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
CITRATE ANION / 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 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,9706
Polymers56,4072
Non-polymers5624
Water5,224290
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3932
Polymers28,2041
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5774
Polymers28,2041
Non-polymers3733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.827, 57.270, 76.927
Angle α, β, γ (deg.)90.00, 95.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase


Mass: 28203.709 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: blaA, blaC, A4S10_02181, DKC2_2191, DSI80_06165, ERS007661_01447, ERS007681_02835, ERS007718_02594, ERS007741_00391, ERS053720_02349
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A045INV3, beta-lactamase
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.18 Å3/Da / Density % sol: 43.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES buffer pH 6.3 0.864 M trisodium citrate (additive)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.4→53.62 Å / Num. obs: 87116 / % possible obs: 95.1 % / Redundancy: 1.4 % / CC1/2: 0.975 / Net I/σ(I): 5
Reflection shellResolution: 1.4→1.43 Å / Num. unique obs: 3041 / CC1/2: 0.335

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Processing

Software
NameVersionClassification
REFMAC1refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→53.62 Å / SU B: 3.053 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.11 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2515 2980 4.9 %RANDOM
Rwork0.23206 ---
obs0.23301 57783 98.66 %-
Displacement parametersBiso mean: 15.535 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20.01 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→53.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3809 0 38 290 4137

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