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- PDB-8rg2: Structure of BlaC from Mycobacterium tuberculosis at pH 8 -

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Basic information

Entry
Database: PDB / ID: 8rg2
TitleStructure of BlaC from Mycobacterium tuberculosis at pH 8
ComponentsBeta-lactamase
KeywordsHYDROLASE / free form Structure of BlaC from Mycobacterium tuberculosis at pH 8
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: 1.8 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 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2024Provider: 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)28,3652
Polymers28,2731
Non-polymers921
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-0 kcal/mol
Surface area10950 Å2
Unit cell
Length a, b, c (Å)54.131, 54.633, 80.140
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: 28272.721 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris pH 8 (buffer) 20%w/v PEG 6K (precipitant) 0.01 M ZnCl2 (salt)

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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 PILATUS 6M-F / Detector: PIXEL / Date: Nov 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.8→38.48 Å / Num. obs: 22101 / % possible obs: 97.6 % / Redundancy: 1.8 % / CC1/2: 0.995 / Net I/σ(I): 9.7
Reflection shellResolution: 1.8→1.84 Å / Num. unique obs: 929 / CC1/2: 0.588

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
autoPROCdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→38.48 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.865 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18853 1088 4.9 %RANDOM
Rwork0.16092 ---
obs0.16235 21009 97.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.609 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.8→38.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1989 0 6 211 2206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122049
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161935
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.6522799
X-RAY DIFFRACTIONr_angle_other_deg0.4991.5684439
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.735268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.876519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55810308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0720.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022485
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02467
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6241.7031066
X-RAY DIFFRACTIONr_mcbond_other1.6131.7011066
X-RAY DIFFRACTIONr_mcangle_it2.4523.0481333
X-RAY DIFFRACTIONr_mcangle_other2.473.0511334
X-RAY DIFFRACTIONr_scbond_it2.582.018983
X-RAY DIFFRACTIONr_scbond_other2.5792.02984
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0653.5591466
X-RAY DIFFRACTIONr_long_range_B_refined5.3420.722410
X-RAY DIFFRACTIONr_long_range_B_other5.2118.622340
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 63 -
Rwork0.245 1141 -
obs--73.41 %

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