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- PDB-7a72: Structure of G132S BlaC from Mycobacterium tuberculosis bound to ... -

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Basic information

Entry
Database: PDB / ID: 7a72
TitleStructure of G132S BlaC from Mycobacterium tuberculosis bound to the trans-enamine adduct of sulbactam
ComponentsBeta-lactamase
KeywordsHYDROLASE / BlaC / beta-lactamase / Mycobacterium tuberculosis / inhibitor
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
ACETATE ION / TRANS-ENAMINE INTERMEDIATE OF SULBACTAM / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)28,9306
Polymers28,3601
Non-polymers5715
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-0 kcal/mol
Surface area10660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.488, 54.658, 78.202
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-TSL / TRANS-ENAMINE INTERMEDIATE OF SULBACTAM


Mass: 235.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13NO5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.02 Å3/Da / Density % sol: 38.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 0.1 M Sodium Cacodylate, 15% PEG-SB, 10% Ethylene Glycol, 5% TMate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.912 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.912 Å / Relative weight: 1
ReflectionResolution: 1.3→78.2 Å / Num. obs: 56098 / % possible obs: 98.2 % / Redundancy: 5.7 % / CC1/2: 0.999 / Rpim(I) all: 0.038 / Net I/σ(I): 11.1
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2775 / CC1/2: 0.655 / Rpim(I) all: 0.582

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H2K

6h2k


Resolution: 1.3→44.84 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.436 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18938 2648 4.7 %RANDOM
Rwork0.15221 ---
obs0.154 53380 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.333 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20 Å20 Å2
2--1.08 Å2-0 Å2
3----2.42 Å2
Refinement stepCycle: 1 / Resolution: 1.3→44.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 37 221 2252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0132111
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171965
X-RAY DIFFRACTIONr_angle_refined_deg1.941.6552877
X-RAY DIFFRACTIONr_angle_other_deg1.6861.5784527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5865273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.66520.354113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.99415316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5931520
X-RAY DIFFRACTIONr_chiral_restr0.1130.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022430
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02458
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_it1.1680.8531084
X-RAY DIFFRACTIONr_mcbond_other1.1680.8511082
X-RAY DIFFRACTIONr_mcangle_it1.4891.2871359
X-RAY DIFFRACTIONr_mcangle_other1.4891.2871360
X-RAY DIFFRACTIONr_scbond_it1.7191.061027
X-RAY DIFFRACTIONr_scbond_other1.7191.0611028
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0631.5281519
X-RAY DIFFRACTIONr_long_range_B_refined2.28512.0012521
X-RAY DIFFRACTIONr_long_range_B_other2.1511.6152485
X-RAY DIFFRACTIONr_rigid_bond_restr3.92134076
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 196 -
Rwork0.324 3979 -
obs--99.55 %
Refinement TLS params.Method: refined / Origin x: 12.0337 Å / Origin y: 2.9499 Å / Origin z: 16.7925 Å
111213212223313233
T0.0028 Å20.0028 Å20.008 Å2-0.007 Å20.0032 Å2--0.0553 Å2
L0.7502 °20.2372 °20.4196 °2-0.6928 °20.1943 °2--0.6961 °2
S-0.0156 Å °0.0166 Å °-0.0153 Å °-0.0103 Å °0.0261 Å °-0.0209 Å °-0.0013 Å °0.0329 Å °-0.0105 Å °

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