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

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Basic information

Entry
Database: PDB / ID: 8gcs
TitleXFEL structure of Mycobacterium tuberculosis beta lactamase microcrystals mixed with sulbactam for 3 ms
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 / 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/transpeptidase-like
Similarity search - Domain/homology
PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis str. Beijing/W BT1 (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsMalla, T.N. / Schmidt, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: 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.
History
DepositionMar 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release

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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)113,9838
Polymers113,6034
Non-polymers3804
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.500, 98.790, 111.470
Angle α, β, γ (deg.)90.000, 108.480, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
d_1ens_1
d_2ens_1
d_3ens_1
d_4ens_1

NCS oper:
IDCodeMatrixVector
1given(-0.99214819223, 0.0388072140175, -0.118894763529), (0.0699751330905, 0.960165692009, -0.27052786296), (0.103660240225, -0.276723407086, -0.955342195534)37.6669117928, -3.91068883552, 37.2682945967
2given(0.798389177785, 0.00581640298328, 0.602113685489), (0.00584180806507, -0.999981105363, 0.0019136863592), (0.60211343954, 0.00198956610512, -0.798408070821)-9.40896425187, -33.9098214687, 28.6981487221
3given(-0.721174936412, -0.118897556649, -0.682473502866), (-0.0819624889566, -0.963597416606, 0.254484123501), (-0.687887244754, 0.239464798526, 0.685177165974)42.8814590865, -29.5174665978, 21.7515572085

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Components

#1: Protein
Beta-lactamase / Ambler class A beta-lactamase


Mass: 28400.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis str. Beijing/W BT1 (bacteria)
Gene: blaC, blaA, BQ2027_MB2094C / Production host: Escherichia coli (E. coli) / References: UniProt: P0A5I7, beta-lactamase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 3.7 Å3/Da / Density % sol: 66.76 %
Crystal growTemperature: 293 K / Method: batch mode / Details: 2.4 M ammonium phosphate

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Data collection

DiffractionMean temperature: 293 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: 2.6→22.01 Å / Num. obs: 42822 / % possible obs: 100 % / Redundancy: 343 % / Biso Wilson estimate: 64.66 Å2 / R split: 0.23 / Net I/σ(I): 4.3
Reflection shellResolution: 2.6→2.7 Å / Mean I/σ(I) obs: 0.13 / Num. unique obs: 5038 / CC1/2: 0.2 / R split: 3.2 / % 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: 2.62→22.01 Å / SU ML: 0.4578 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.7305
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2661 2165 5.12 %
Rwork0.2059 40105 -
obs0.209 42270 84.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.61 Å2
Refinement stepCycle: LAST / Resolution: 2.62→22.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7952 0 20 152 8124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00898124
X-RAY DIFFRACTIONf_angle_d1.083911092
X-RAY DIFFRACTIONf_chiral_restr0.05311276
X-RAY DIFFRACTIONf_plane_restr0.011468
X-RAY DIFFRACTIONf_dihedral_angle_d6.18751168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.680.599590.512152X-RAY DIFFRACTION4.86
2.68-2.750.3845470.3775926X-RAY DIFFRACTION29.59
2.75-2.820.36251130.36931841X-RAY DIFFRACTION58.73
2.82-2.90.37531430.38292531X-RAY DIFFRACTION80.88
2.9-30.38171560.32873030X-RAY DIFFRACTION96.6
3-3.10.362030.28623123X-RAY DIFFRACTION99.76
3.1-3.230.34471660.27993138X-RAY DIFFRACTION100
3.23-3.370.33461510.25663174X-RAY DIFFRACTION100
3.37-3.550.31560.21583140X-RAY DIFFRACTION99.94
3.55-3.770.28751440.19283178X-RAY DIFFRACTION100
3.77-4.060.2591770.17563154X-RAY DIFFRACTION100
4.06-4.470.21661940.15723150X-RAY DIFFRACTION100
4.47-5.110.24351490.15163188X-RAY DIFFRACTION100
5.11-6.410.23541710.18913175X-RAY DIFFRACTION100
6.41-22.010.19821860.17833205X-RAY DIFFRACTION99.24

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