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

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Basic information

Entry
Database: PDB / ID: 8gct
TitleXFEL structure of Mycobacterium tuberculosis beta lactamase microcrystals mixed with sulbactam for 6 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 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: 2.75 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
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.440, 98.810, 112.010
Angle α, β, γ (deg.)90.000, 108.670, 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(-0.993530714265, 0.0440463742467, -0.104673954393), (0.070930166988, 0.960505486276, -0.269068991607), (0.0886883939619, -0.274752848482, -0.957415918516)37.4352503443, -4.06801264152, 37.7844484205
2given(0.795849085027, 0.00662104085753, 0.605458830706), (0.00679354124914, -0.99997491259, 0.00200548923223), (0.605456919739, 0.00251714277056, -0.795874099549)-9.54091052681, -33.7636340818, 28.7943586236
3given(-0.727933792924, -0.114356012994, -0.676043708211), (-0.0841459039602, -0.963639981345, 0.253608858679), (-0.680464444307, 0.241496767362, 0.691843516547)42.9635400811, -29.1695949436, 21.5129509057

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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.: 171 / 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: 3.71 Å3/Da / Density % sol: 66.87 %
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: 2.75→20.53 Å / Num. obs: 43284 / % possible obs: 100 % / Redundancy: 144 % / Biso Wilson estimate: 64.55 Å2 / CC1/2: 0.96 / R split: 0.24 / Net I/σ(I): 4.11
Reflection shellResolution: 2.75→2.9 Å / Rmerge(I) obs: 3.54 / Num. unique obs: 4344 / CC1/2: 0.15 / % possible all: 100
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: 2.75→20.53 Å / SU ML: 0.4943 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.7169
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2596 2149 5.09 %
Rwork0.2147 40042 -
obs0.217 42191 97.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.52 Å2
Refinement stepCycle: LAST / Resolution: 2.75→20.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7952 0 20 171 8143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00218124
X-RAY DIFFRACTIONf_angle_d0.516711092
X-RAY DIFFRACTIONf_chiral_restr0.03941276
X-RAY DIFFRACTIONf_plane_restr0.00381468
X-RAY DIFFRACTIONf_dihedral_angle_d4.33411168
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.673936005605
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.517478931355
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.653056400425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.810.38761150.34832100X-RAY DIFFRACTION76.48
2.81-2.880.36791290.3562456X-RAY DIFFRACTION90.67
2.88-2.960.40211520.34832631X-RAY DIFFRACTION97.1
2.96-3.050.35411540.31632703X-RAY DIFFRACTION99.55
3.05-3.150.35551620.28622688X-RAY DIFFRACTION99.86
3.15-3.260.29311420.27282735X-RAY DIFFRACTION100
3.26-3.390.3071310.2452750X-RAY DIFFRACTION100
3.39-3.540.2741360.21862740X-RAY DIFFRACTION99.93
3.54-3.730.24341080.19742765X-RAY DIFFRACTION100
3.73-3.960.26261510.19382725X-RAY DIFFRACTION100
3.96-4.260.26271620.17682719X-RAY DIFFRACTION100
4.26-4.690.21861600.17082729X-RAY DIFFRACTION100
4.69-5.350.23651240.17852772X-RAY DIFFRACTION99.97
5.36-6.710.23831570.20752756X-RAY DIFFRACTION99.97
6.71-20.530.19311660.18972773X-RAY DIFFRACTION99.66

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