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- PDB-7bh4: XFEL structure of apo CTX-M-15 after mixing for 0.7 sec with erta... -

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Basic information

Entry
Database: PDB / ID: 7bh4
TitleXFEL structure of apo CTX-M-15 after mixing for 0.7 sec with ertapenem using a piezoelectric injector (PolyPico)
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / serial crystallography / beta-lactamase / antibiotic / ertapenem / XFEL
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / membrane
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
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsHinchliffe, P. / Tooke, C.L. / Butryn, A. / Spencer, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/J014400/1 United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: An on-demand, drop-on-drop method for studying enzyme catalysis by serial crystallography.
Authors: Butryn, A. / Simon, P.S. / Aller, P. / Hinchliffe, P. / Massad, R.N. / Leen, G. / Tooke, C.L. / Bogacz, I. / Kim, I.S. / Bhowmick, A. / Brewster, A.S. / Devenish, N.E. / Brem, J. / Kamps, J. ...Authors: Butryn, A. / Simon, P.S. / Aller, P. / Hinchliffe, P. / Massad, R.N. / Leen, G. / Tooke, C.L. / Bogacz, I. / Kim, I.S. / Bhowmick, A. / Brewster, A.S. / Devenish, N.E. / Brem, J. / Kamps, J.J.A.G. / Lang, P.A. / Rabe, P. / Axford, D. / Beale, J.H. / Davy, B. / Ebrahim, A. / Orlans, J. / Storm, S.L.S. / Zhou, T. / Owada, S. / Tanaka, R. / Tono, K. / Evans, G. / Owen, R.L. / Houle, F.A. / Sauter, N.K. / Schofield, C.J. / Spencer, J. / Yachandra, V.K. / Yano, J. / Kern, J.F. / Orville, A.M.
History
DepositionJan 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3892
Polymers28,2931
Non-polymers961
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-17 kcal/mol
Surface area10890 Å2
Unit cell
Length a, b, c (Å)44.932, 45.613, 117.668
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Beta-lactamase


Mass: 28292.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaCTX-M-15 / Production host: Escherichia coli (E. coli) / Strain (production host): SoluBL21 / References: UniProt: G3G192, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.13 Å3/Da / Density % sol: 42.28 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 2.0 M ammonium sulphate, 0.1 M Tris 8.0

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Data collection

DiffractionMean temperature: 303 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.2406 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2406 Å / Relative weight: 1
ReflectionResolution: 1.55→58.83 Å / Num. obs: 35926 / % possible obs: 100 % / Redundancy: 114.15 % / Biso Wilson estimate: 21.29 Å2 / CC1/2: 0.949 / R split: 0.237 / Net I/σ(I): 36.063
Reflection shellResolution: 1.55→1.58 Å / Mean I/σ(I) obs: 0.86 / Num. unique obs: 1756 / CC1/2: 0.103 / R split: 1.163
Serial crystallography measurementFocal spot size: 1.4 µm2 / Pulse duration: 10 fsec. / Pulse energy: 450 µJ / Pulse photon energy: 10 keV
Serial crystallography sample deliveryDescription: Acoustic droplet ejection on conveyor belt with mixing using a pizoelectric injector
Method: injection

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
cctbx.xfeldata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6qw8

6qw8


Resolution: 1.55→32.01 Å / SU ML: 0.311 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.2598
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.206 1769 4.94 %
Rwork0.1789 34069 -
obs0.1803 35838 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.74 Å2
Refinement stepCycle: LAST / Resolution: 1.55→32.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1942 0 5 158 2105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00972008
X-RAY DIFFRACTIONf_angle_d1.02772730
X-RAY DIFFRACTIONf_chiral_restr0.0558318
X-RAY DIFFRACTIONf_plane_restr0.0071359
X-RAY DIFFRACTIONf_dihedral_angle_d19.0187753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.44351150.42592538X-RAY DIFFRACTION98.3
1.59-1.640.42361560.38762534X-RAY DIFFRACTION98.53
1.64-1.690.34681360.31852584X-RAY DIFFRACTION99.74
1.69-1.750.32451330.25942577X-RAY DIFFRACTION99.93
1.75-1.820.27671270.23292610X-RAY DIFFRACTION100
1.82-1.910.28481350.21832588X-RAY DIFFRACTION100
1.91-2.010.23861460.19092598X-RAY DIFFRACTION100
2.01-2.130.21451010.18352656X-RAY DIFFRACTION100
2.13-2.30.20631460.17622607X-RAY DIFFRACTION100
2.3-2.530.20821240.17012653X-RAY DIFFRACTION100
2.53-2.890.19241500.16822628X-RAY DIFFRACTION100
2.89-3.640.18871660.14932655X-RAY DIFFRACTION100
3.64-32.010.141340.14122841X-RAY DIFFRACTION99.97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.44143930317-0.0530473148263-0.4626631433891.029952846510.1198807304760.675027889301-0.0299691190762-0.0275369537296-0.0504200647284-0.00839673195690.0296509622483-0.01554454128710.04856888358540.06622864368440.02130377145610.160511722727-0.00427707715003-0.001873809705340.1628047378870.01799213052210.132867224232-2.04569013108-14.640375170717.2802493693
22.469214022520.255188815263-1.122202125886.144159872034.221954823483.58603936687-0.04781741781650.3017120143280.270942215899-0.417307706790.05171509792920.498333890293-0.397692649587-0.1555043650850.04726979489630.239015522360.0154818222835-0.02872654871930.2155480001260.03827468251560.274441284818-15.65120082137.7318513937718.5109173455
30.4714832707550.0749001795382-0.1783542114641.0358638050.3050840538420.6858303521440.00136514704265-0.0163317938970.0248205195348-0.0123955045719-0.003444934499680.0551445698946-0.0069706181932-0.02530657888090.003011742843280.1455386644990.000532567686936-0.001762652439820.1574666554390.008045459134790.14652109591-6.16622151582-10.028915518420.0026583991
42.097243184061.75831739056-2.942157069892.86036557015-4.005081225185.83236058633-0.02473355291060.14336254711-0.015548787775-0.2585512145110.08056390247090.02821746029880.1395007951440.0339635195419-0.04967880455540.203280581870.0300209438618-0.0004358017044560.187153600909-0.001970285381560.174684148487-2.33541405856-14.86287196987.71446488828
59.6595615154-2.907949409980.4778421483133.84795940176-3.660716935474.18452050630.08588499642090.273589800682-0.176995779274-0.5185375803120.1085546631320.1595474176060.3491071715110.0928621608549-0.115253705090.251523060365-0.01046205631630.0003785376820880.178483941383-0.03031604069490.126286992474-3.54145827423-19.63822333413.11925987118
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 96 )
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 115 )
3X-RAY DIFFRACTION3chain 'A' and (resid 116 through 250 )
4X-RAY DIFFRACTION4chain 'A' and (resid 251 through 273 )
5X-RAY DIFFRACTION5chain 'A' and (resid 274 through 286 )

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