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- PDB-8rfz: Structure of E166A BlaC from Mycobacterium tuberculosis at pH 4.5 -

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Basic information

Entry
Database: PDB / ID: 8rfz
TitleStructure of E166A BlaC from Mycobacterium tuberculosis at pH 4.5
ComponentsBeta-lactamase
KeywordsHYDROLASE / Beta-lactamase from Mycobacterium tuberculosis and encoded by blaC gene
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: 1.42 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)28,4073
Polymers28,2151
Non-polymers1922
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-34 kcal/mol
Surface area10840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.955, 54.745, 53.759
Angle α, β, γ (deg.)90.00, 92.89, 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: 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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.03 Å3/Da / Density % sol: 39.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.05 M LiSO4 (Salt) 0.1 M Na Acet 4.5 pH (Buffer) 25 %w/v PEG 8K (Precipitant)

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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 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.42→54.74 Å / Num. obs: 42647 / % possible obs: 99.3 % / Redundancy: 1.4 % / CC1/2: 0.853 / Rpim(I) all: 0.161 / Net I/σ(I): 8
Reflection shellResolution: 1.42→1.44 Å / Num. unique obs: 2384 / CC1/2: 0.575 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→38.36 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.881 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21056 2384 5.6 %RANDOM
Rwork0.18897 ---
obs0.19023 40243 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.809 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å2-0 Å20.73 Å2
2---0.06 Å2-0 Å2
3----2.02 Å2
Refinement stepCycle: 1 / Resolution: 1.42→38.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1985 0 10 241 2236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122032
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161910
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.6512776
X-RAY DIFFRACTIONr_angle_other_deg0.5141.5694378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4075264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.178519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41510302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022454
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02462
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_it1.3441.5921059
X-RAY DIFFRACTIONr_mcbond_other1.3441.5921059
X-RAY DIFFRACTIONr_mcangle_it1.9292.8621322
X-RAY DIFFRACTIONr_mcangle_other1.9282.8631323
X-RAY DIFFRACTIONr_scbond_it2.2131.796973
X-RAY DIFFRACTIONr_scbond_other2.0881.784966
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0823.1971443
X-RAY DIFFRACTIONr_long_range_B_refined4.67219.382403
X-RAY DIFFRACTIONr_long_range_B_other4.36517.422319
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.42→1.454 Å
RfactorNum. reflection% reflection
Rfree0.274 193 -
Rwork0.293 2875 -
obs--97.09 %

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