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- PDB-7a71: Structure of G132S BlaC from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 7a71
TitleStructure of G132S 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 / beta-lactamase activity / 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
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 27, 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

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,35311
Polymers28,3601
Non-polymers99310
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-32 kcal/mol
Surface area11010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.296, 54.316, 78.852
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


Mass: 28359.801 Da / Num. of mol.: 1
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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.01 Å3/Da / Density % sol: 38.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Sodium Cacodylate, 0.2 M Sodium Chloride, 2 M Ammonium Sulfate

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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 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→44.73 Å / Num. obs: 45293 / % possible obs: 98.9 % / Redundancy: 3.7 % / CC1/2: 0.989 / Rpim(I) all: 0.083 / Net I/σ(I): 8.3
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2169 / CC1/2: 0.654 / Rpim(I) all: 0.698

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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→44.77 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.999 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16083 2154 4.8 %RANDOM
Rwork0.13004 ---
obs0.13153 43081 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å2-0 Å2
2---0.02 Å20 Å2
3---0.26 Å2
Refinement stepCycle: 1 / Resolution: 1.4→44.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 61 201 2256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5570.3681091
X-RAY DIFFRACTIONr_mcbond_other0.5430.3651088
X-RAY DIFFRACTIONr_mcangle_it0.7820.5551364
X-RAY DIFFRACTIONr_mcangle_other0.7840.5561365
X-RAY DIFFRACTIONr_scbond_it1.6360.6031054
X-RAY DIFFRACTIONr_scbond_other1.3430.5721039
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5010.7891533
X-RAY DIFFRACTIONr_long_range_B_refined1.8585.8812530
X-RAY DIFFRACTIONr_long_range_B_other1.6925.5332495
X-RAY DIFFRACTIONr_rigid_bond_restr3.93734147
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
Rfree0.253 144 -
Rwork0.218 3084 -
obs--96.7 %
Refinement TLS params.Method: refined / Origin x: -12.1323 Å / Origin y: -2.7733 Å / Origin z: 17.1626 Å
111213212223313233
T0.0026 Å20.0011 Å2-0.0076 Å2-0.0012 Å2-0.0038 Å2--0.0228 Å2
L0.6654 °20.1098 °2-0.3322 °2-0.5717 °2-0.1776 °2--0.5746 °2
S-0.0067 Å °0.0139 Å °-0.0001 Å °-0.0056 Å °0.008 Å °0.0155 Å °0.0039 Å °-0.0164 Å °-0.0013 Å °

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