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- PDB-8ebi: XFEL structure of beta lactamase microcrystals mixed with sulbact... -

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Basic information

Entry
Database: PDB / ID: 8ebi
TitleXFEL structure of beta lactamase microcrystals mixed with sulbactam solution for 15ms
ComponentsBeta-lactamase
KeywordsHYDROLASE / Beta lactamase
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: 2.7 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
DepositionAug 31, 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 20, 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)114,45410
Polymers113,6034
Non-polymers8506
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.300, 98.560, 112.050
Angle α, β, γ (deg.)90.000, 108.780, 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.: 2 / Source method: obtained synthetically / Formula: C8H13NO5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 3.7 Å3/Da / Density % sol: 66.71 %
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: Y
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: 2.65→20.86 Å / Num. obs: 41529 / % possible obs: 100 % / Redundancy: 273 % / Biso Wilson estimate: 63.35 Å2 / CC star: 0.98 / R split: 0.23 / Net I/σ(I): 4.5
Reflection shellResolution: 2.65→2.75 Å / Redundancy: 130 % / Num. unique obs: 4080 / CC star: 0.58 / R split: 3.16 / % possible all: 100
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
REFMAC5refinement
PHENIX1.19.2_4158refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6b5x

6b5x


Resolution: 2.7→20.86 Å / SU ML: 0.5178 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.5327
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2805 2064 4.97 %
Rwork0.2292 39465 -
obs0.2317 41529 91.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7952 0 50 156 8158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00298152
X-RAY DIFFRACTIONf_angle_d0.618311130
X-RAY DIFFRACTIONf_chiral_restr0.04211278
X-RAY DIFFRACTIONf_plane_restr0.00541474
X-RAY DIFFRACTIONf_dihedral_angle_d6.8081184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.3851920.33971669X-RAY DIFFRACTION58.2
2.77-2.840.36671020.36452057X-RAY DIFFRACTION72.84
2.84-2.910.43181280.38222403X-RAY DIFFRACTION83.7
2.91-30.41621460.36542676X-RAY DIFFRACTION94.13
3-3.090.44391450.3992648X-RAY DIFFRACTION92.03
3.09-3.20.38121340.32162770X-RAY DIFFRACTION97.06
3.2-3.330.33881420.27812779X-RAY DIFFRACTION97.89
3.33-3.480.29961400.23872820X-RAY DIFFRACTION97.5
3.48-3.670.25121670.20462748X-RAY DIFFRACTION97.13
3.67-3.890.25521340.20582786X-RAY DIFFRACTION97.37
3.89-4.190.24261390.18312790X-RAY DIFFRACTION96.73
4.19-4.610.21491770.17312738X-RAY DIFFRACTION96.94
4.61-5.270.25081330.18672805X-RAY DIFFRACTION96.71
5.27-6.60.27641500.22582841X-RAY DIFFRACTION97.78
6.6-20.860.23221350.1872935X-RAY DIFFRACTION99.42

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