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

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Basic information

Entry
Database: PDB / ID: 8gcv
TitleXFEL structure of Mycobacterium tuberculosis beta lactamase microcrystals
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/transpeptidase-like
Similarity search - Domain/homology
PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.2 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
Water9,206511
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.640, 98.090, 110.880
Angle α, β, γ (deg.)90.000, 108.450, 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-IDDetails
d_1ens_1(chain "A" and (resid 30 through 35 or resid 37...
d_2ens_1(chain "B" and (resid 30 through 35 or resid 37...
d_3ens_1(chain "C" and (resid 30 through 35 or resid 37...
d_4ens_1(chain "D" and (resid 30 through 35 or resid 37...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LEUALAA2 - 7
d_12ens_1LEUARGA9 - 11
d_13ens_1TYRILEA13 - 72
d_14ens_1SERASNA74 - 144
d_15ens_1ASPALAA146 - 265
d_16ens_1PO4PO4B
d_21ens_1LEUALAC2 - 7
d_22ens_1LEUARGC9 - 11
d_23ens_1TYRILEC13 - 72
d_24ens_1SERASNC74 - 144
d_25ens_1ASPALAC146 - 265
d_26ens_1PO4PO4D
d_31ens_1LEUALAE2 - 7
d_32ens_1LEUARGE9 - 11
d_33ens_1TYRILEE13 - 72
d_34ens_1SERASNE74 - 144
d_35ens_1ASPALAE146 - 265
d_36ens_1PO4PO4F
d_41ens_1LEUALAG2 - 7
d_42ens_1LEUARGG9 - 11
d_43ens_1TYRILEG13 - 72
d_44ens_1SERASNG74 - 144
d_45ens_1ASPALAG146 - 265
d_46ens_1PO4PO4H

NCS oper:
IDCodeMatrixVector
1given(-0.994056401751, 0.0507486547406, -0.0963142989406), (0.0754379496683, 0.958964023902, -0.273307732441), (0.0784919479198, -0.278949054316, -0.95709270147)37.1879584401, -4.09520126423, 37.6885712625
2given(0.799455798029, 0.00498848849909, 0.600704205063), (0.00525445076226, -0.999985335489, 0.00131131796873), (0.600701937524, 0.00210802991502, -0.799470286168)-9.4489293172, -33.6139806041, 28.8032449597
3given(-0.738047885635, -0.111740060356, -0.665431797724), (-0.0873532821061, -0.962070334715, 0.258437758787), (-0.669070043131, 0.24886709299, 0.700293115354)42.7406077965, -29.0994762511, 21.1733540378

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 3.62 Å3/Da / Density % sol: 65.99 %
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: 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: 2.2→22.14 Å / Num. obs: 83447 / % possible obs: 100 % / Redundancy: 453 % / Biso Wilson estimate: 53.27 Å2 / Rmerge(I) obs: 0.23 / Net I/σ(I): 4.38
Reflection shellResolution: 2.2→2.3 Å / Num. unique obs: 8251 / CC1/2: 0.3
Serial crystallography sample deliveryMethod: injection

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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: 2.2→22.14 Å / SU ML: 0.4454 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.8464
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2605 3459 5.04 %
Rwork0.2195 65163 -
obs0.2216 68622 83.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.32 Å2
Refinement stepCycle: LAST / Resolution: 2.2→22.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7952 0 20 511 8483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00848124
X-RAY DIFFRACTIONf_angle_d1.023311092
X-RAY DIFFRACTIONf_chiral_restr0.0581276
X-RAY DIFFRACTIONf_plane_restr0.0091468
X-RAY DIFFRACTIONf_dihedral_angle_d14.26452916
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.655240977114
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.517523862797
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.577378049115
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.395330.3906701X-RAY DIFFRACTION22.23
2.23-2.260.3764460.4066838X-RAY DIFFRACTION27.17
2.26-2.30.411470.3817974X-RAY DIFFRACTION31.27
2.3-2.330.4274560.39111330X-RAY DIFFRACTION42.28
2.33-2.370.35631160.37791869X-RAY DIFFRACTION60.87
2.37-2.410.41711240.38082084X-RAY DIFFRACTION67.79
2.41-2.450.34961300.37172088X-RAY DIFFRACTION67.77
2.45-2.50.3841400.36112558X-RAY DIFFRACTION82.46
2.5-2.550.35191630.36292902X-RAY DIFFRACTION93.25
2.55-2.610.39081720.35372961X-RAY DIFFRACTION96.1
2.61-2.670.34871660.33133062X-RAY DIFFRACTION98.56
2.67-2.740.39841640.34253116X-RAY DIFFRACTION99.61
2.74-2.810.4041560.32133081X-RAY DIFFRACTION99.66
2.81-2.890.32171870.30353071X-RAY DIFFRACTION99.69
2.89-2.980.33611570.28123122X-RAY DIFFRACTION100
2.98-3.090.30531760.26013114X-RAY DIFFRACTION100
3.09-3.210.3021460.23193130X-RAY DIFFRACTION100
3.21-3.360.23031410.21733163X-RAY DIFFRACTION100
3.36-3.540.2321650.19263099X-RAY DIFFRACTION99.94
3.54-3.760.24621500.18143143X-RAY DIFFRACTION99.97
3.76-4.050.21191860.17663101X-RAY DIFFRACTION100
4.05-4.450.20741700.16453143X-RAY DIFFRACTION100
4.45-5.090.19461590.15813140X-RAY DIFFRACTION99.97
5.09-6.380.24681600.18563156X-RAY DIFFRACTION100
6.38-22.140.21151490.18263217X-RAY DIFFRACTION99.59

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