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- PDB-8ec4: XFEL structure of Mycobacterium tuberculosis beta lactamase micro... -

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Basic information

Entry
Database: PDB / ID: 8ec4
TitleXFEL structure of Mycobacterium tuberculosis beta lactamase microcrystals mixed with sulbactam for 240ms
ComponentsBeta-lactamase
KeywordsHYDROLASE/Inhibitor / Beta lactamase / sulbactam / inhibitor / HYDROLASE / HYDROLASE-Inhibitor complex
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 / TRANS-ENAMINE INTERMEDIATE OF SULBACTAM / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMalla, T.N. / Schmidt, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
Citation
Journal: Nat Commun / Year: 2023
Title: Heterogeneity in M. tuberculosis beta-lactamase inhibition by Sulbactam.
Authors: Malla, T.N. / Zielinski, K. / Aldama, L. / Bajt, S. / Feliz, D. / Hayes, B. / Hunter, M. / Kupitz, C. / Lisova, S. / Knoska, J. / Martin-Garcia, J.M. / Mariani, V. / Pandey, S. / Poudyal, I. ...Authors: Malla, T.N. / Zielinski, K. / Aldama, L. / Bajt, S. / Feliz, D. / Hayes, B. / Hunter, M. / Kupitz, C. / Lisova, S. / Knoska, J. / Martin-Garcia, J.M. / Mariani, V. / Pandey, S. / Poudyal, I. / Sierra, R.G. / Tolstikova, A. / Yefanov, O. / Yoon, C.H. / Ourmazd, A. / Fromme, P. / Schwander, P. / Barty, A. / Chapman, H.N. / Stojkovic, E.A. / Batyuk, A. / Boutet, S. / Phillips Jr., G.N. / Pollack, L. / Schmidt, M.
#1: Journal: Res Sq / Year: 2023
Title: Heterogeneity in the M. tuberculosis beta-Lactamase Inhibition by Sulbactam.
Authors: Schmidt, M. / Malla, T.N. / Zielinski, K. / Aldama, L. / Bajt, S. / Feliz, D. / Hayes, B. / Hunter, M. / Kupitz, C. / Lisova, S. / Knoska, J. / Martin-Garcia, J. / Mariani, V. / Pandey, S. / ...Authors: Schmidt, M. / Malla, T.N. / Zielinski, K. / Aldama, L. / Bajt, S. / Feliz, D. / Hayes, B. / Hunter, M. / Kupitz, C. / Lisova, S. / Knoska, J. / Martin-Garcia, J. / Mariani, V. / Pandey, S. / Poudyal, I. / Sierra, R. / Tolstikova, A. / Yefanov, O. / Yoon, C.H. / Ourmazd, A. / Fromme, P. / Schwander, P. / Barty, A. / Chapman, H. / Stojkovic, E. / Batyuk, A. / Boutet, S. / Phillips, G. / Pollack, L.
History
DepositionSep 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Nov 13, 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

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,92412
Polymers113,6034
Non-polymers1,3218
Water5,350297
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.820, 97.890, 113.170
Angle α, β, γ (deg.)90.000, 109.340, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Beta-lactamase


Mass: 28400.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: blaC, ERS027646_02769 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A655AHQ9, beta-lactamase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-TSL / TRANS-ENAMINE INTERMEDIATE OF SULBACTAM


Mass: 235.258 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H13NO5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 3.67 Å3/Da / Density % sol: 66.51 %
Crystal growTemperature: 300 K / Method: batch mode / pH: 4.1 / Details: 2.4 M ammonium phosphate

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Data collection

DiffractionMean temperature: 300 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.26 Å
DetectorType: SLAC ePix10k 2M / Detector: PIXEL / Date: Oct 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.26 Å / Relative weight: 1
ReflectionResolution: 2.35→22.42 Å / Num. obs: 68441 / % possible obs: 100 % / Redundancy: 446 % / Biso Wilson estimate: 57.97 Å2 / CC1/2: 0.97 / CC star: 0.99 / Net I/σ(I): 3.78
Reflection shellResolution: 2.35→2.43 Å / Num. unique obs: 6775 / CC1/2: 0.25 / CC star: 0.64 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6b5x

6b5x


Resolution: 2.35→22.42 Å / SU ML: 0.4807 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.3204
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2747 2696 5.02 %
Rwork0.2408 50986 -
obs0.2425 53682 78.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.88 Å2
Refinement stepCycle: LAST / Resolution: 2.35→22.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7952 0 80 297 8329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028180
X-RAY DIFFRACTIONf_angle_d0.801811168
X-RAY DIFFRACTIONf_chiral_restr0.03891280
X-RAY DIFFRACTIONf_plane_restr0.00361480
X-RAY DIFFRACTIONf_dihedral_angle_d6.32511200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.390.4226780.41031375X-RAY DIFFRACTION41.02
2.39-2.440.296930.485730X-RAY DIFFRACTION0.93
2.44-2.490.4116150.4077451X-RAY DIFFRACTION13.16
2.49-2.540.3425630.38211318X-RAY DIFFRACTION38.74
2.54-2.60.4243600.39661446X-RAY DIFFRACTION42.01
2.6-2.670.43611150.38392454X-RAY DIFFRACTION71.1
2.67-2.740.33571640.38243099X-RAY DIFFRACTION90.34
2.74-2.820.33691670.38063206X-RAY DIFFRACTION95.44
2.82-2.910.40751650.37273298X-RAY DIFFRACTION96.79
2.91-3.010.39611710.34853431X-RAY DIFFRACTION99.64
3.01-3.130.40691630.32153421X-RAY DIFFRACTION99.94
3.13-3.280.36271680.2853435X-RAY DIFFRACTION99.97
3.28-3.450.29021990.2493418X-RAY DIFFRACTION100
3.45-3.660.26171860.2153415X-RAY DIFFRACTION100
3.66-3.940.25031770.20913429X-RAY DIFFRACTION100
3.94-4.340.21981930.1893410X-RAY DIFFRACTION99.97
4.34-4.960.21771810.1813450X-RAY DIFFRACTION99.97
4.96-6.230.25142120.21523422X-RAY DIFFRACTION99.89
6.23-22.420.23452160.19863478X-RAY DIFFRACTION99.81

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