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- PDB-7a5t: Crystal structure of A55E mutant of BlaC from Mycobacterium tuber... -

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Basic information

Entry
Database: PDB / ID: 7a5t
TitleCrystal structure of A55E mutant of BlaC from Mycobacterium tuberculosis
ComponentsBeta-lactamase
KeywordsHYDROLASE / BlaC / beta-lactamase / Mycobacterium tuberculosis
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsChikunova, A. / Ahmad, M.U. / Perrakis, A. / Ubbink, M.
Funding support Netherlands, 2items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)ECHO-711.016.002 Netherlands
H2020 Marie Curie Actions of the European Commission653706 Netherlands
CitationJournal: Biochemistry / Year: 2021
Title: The G132S Mutation Enhances the Resistance of Mycobacterium tuberculosis beta-Lactamase against Sulbactam.
Authors: van Alen, I. / Chikunova, A. / Safeer, A.A. / Ahmad, M.U.D. / Perrakis, A. / Ubbink, M.
History
DepositionAug 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)29,31211
Polymers28,3881
Non-polymers92410
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-10 kcal/mol
Surface area10980 Å2
Unit cell
Length a, b, c (Å)38.990, 54.356, 53.687
Angle α, β, γ (deg.)90.00, 91.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase


Mass: 28387.812 Da / Num. of mol.: 1 / Mutation: A55E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: blaC, ERS027646_02769 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A655AHQ9, beta-lactamase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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 Å3/Da / Density % sol: 38.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.8 M Disodium Succinate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→38.21 Å / Num. obs: 42718 / % possible obs: 96.9 % / Redundancy: 2.5 % / CC1/2: 0.985 / Rpim(I) all: 0.078 / Net I/σ(I): 5.2
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 2.3 % / Num. unique obs: 2050 / CC1/2: 0.752 / Rpim(I) all: 0.344 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GDN

2gdn


Resolution: 1.4→38.21 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.634 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17725 2079 4.9 %RANDOM
Rwork0.14758 ---
obs0.14896 40621 96.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.519 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20.23 Å2
2--0.41 Å2-0 Å2
3----0.61 Å2
Refinement stepCycle: 1 / Resolution: 1.4→38.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 59 207 2262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132100
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171973
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.652847
X-RAY DIFFRACTIONr_angle_other_deg1.6371.584547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8135266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.65120.727110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.33615311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4021520
X-RAY DIFFRACTIONr_chiral_restr0.0980.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022349
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02443
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_it0.6480.4141067
X-RAY DIFFRACTIONr_mcbond_other0.6420.4131066
X-RAY DIFFRACTIONr_mcangle_it0.8880.6241329
X-RAY DIFFRACTIONr_mcangle_other0.8880.6251330
X-RAY DIFFRACTIONr_scbond_it1.2850.5981033
X-RAY DIFFRACTIONr_scbond_other1.2620.5911030
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4530.8221512
X-RAY DIFFRACTIONr_long_range_B_refined1.8666.3372449
X-RAY DIFFRACTIONr_long_range_B_other1.7655.952406
X-RAY DIFFRACTIONr_rigid_bond_restr4.81434073
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 155 -
Rwork0.217 2937 -
obs--94.85 %
Refinement TLS params.Method: refined / Origin x: -16.2774 Å / Origin y: 9.7608 Å / Origin z: -14.6422 Å
111213212223313233
T0.0417 Å2-0.0027 Å2-0.0214 Å2-0.0024 Å20.0028 Å2--0.017 Å2
L0.7891 °2-0.1646 °2-0.4463 °2-0.5271 °20.1264 °2--0.6239 °2
S-0.0058 Å °-0.0385 Å °-0.0013 Å °0.0339 Å °0.0076 Å °-0.0052 Å °0.0013 Å °0.0161 Å °-0.0018 Å °

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