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- PDB-8bv4: Structure of BlaC from Mycobacterium tuberculosis in complex with... -

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Basic information

Entry
Database: PDB / ID: 8bv4
TitleStructure of BlaC from Mycobacterium tuberculosis in complex with vaborbactam
ComponentsBeta-lactamase
KeywordsHYDROLASE
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / periplasmic space / response to antibiotic / extracellular region
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
Vaborbactam / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsChikunova, A. / Bruenle, S. / Ubbink, M.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)ECHO-711.016.002 Netherlands
CitationJournal: Febs J. / Year: 2023
Title: Asp179 in the class A beta-lactamase from Mycobacterium tuberculosis is a conserved yet not essential residue due to epistasis.
Authors: van Alen, I. / Chikunova, A. / van Zanten, D.B. / de Block, A.A. / Timmer, M. / Brunle, S. / Ubbink, M.
History
DepositionDec 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 7, 2024Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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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)29,60013
Polymers28,2731
Non-polymers1,32712
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-39 kcal/mol
Surface area10720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.490, 54.656, 78.109
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 (strain ATCC 25618 / H37Rv) (bacteria)
Gene: blaC, blaA, MRA_2082 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5U493, beta-lactamase
#2: Chemical ChemComp-4D6 / Vaborbactam / {(3R,6S)-2-hydroxy-3-[(thiophen-2-ylacetyl)amino]-1,2-oxaborinan-6-yl}acetic acid / 2-((3R,6S)-2-hydroxy-3-(2-(thiophen-2-yl)acetamido)-1,2-oxaborinan-6-yl)acetic acid / 2-[(3R,6S)-2-hydroxy-3-[(2-thiophen-2-ylacetyl)amino]oxaborinan-6-yl]acetic acid / 1,2-Oxaborinane-6-acetic acid, 2-hydroxy-3-((2-(2-thienyl)acetyl)amino)-, (3R,6S)-


Mass: 297.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16BNO5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic, inhibitor*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: PO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 38.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M MES/Imidazole buffer pH 8.5, 30% w/v EDO-P8K, 0.09M NPS (sodium nitrate, disodium hydrogen phosphate, ammonium sulfate)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→44.82 Å / Num. obs: 17259 / % possible obs: 99.9 % / Redundancy: 1.9 % / CC1/2: 0.985 / Rpim(I) all: 0.124 / Net I/σ(I): 6.5
Reflection shellResolution: 1.95→2 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1172 / CC1/2: 0.703 / Rpim(I) all: 0.566

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GDN

2gdn


Resolution: 1.95→44.82 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.02 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22972 847 4.9 %RANDOM
Rwork0.18822 ---
obs0.19027 16408 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.154 Å2
Baniso -1Baniso -2Baniso -3
1--3.05 Å2-0 Å2-0 Å2
2---3 Å20 Å2
3---6.06 Å2
Refinement stepCycle: 1 / Resolution: 1.95→44.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 80 140 2208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122107
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161896
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.6552870
X-RAY DIFFRACTIONr_angle_other_deg0.4951.5614402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8785266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.901520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49610305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022425
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02404
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_it2.1682.8621064
X-RAY DIFFRACTIONr_mcbond_other2.1612.8621064
X-RAY DIFFRACTIONr_mcangle_it3.0354.2891330
X-RAY DIFFRACTIONr_mcangle_other3.0344.291331
X-RAY DIFFRACTIONr_scbond_it3.0113.2321043
X-RAY DIFFRACTIONr_scbond_other2.6893.1631020
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8584.6341505
X-RAY DIFFRACTIONr_long_range_B_refined6.61547.4652440
X-RAY DIFFRACTIONr_long_range_B_other6.31645.7782399
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 45 -
Rwork0.337 1182 -
obs--99.51 %

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