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- PDB-7bh5: XFEL structure of the ertapenem-derived CTX-M-15 acylenzyme after... -

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Basic information

Entry
Database: PDB / ID: 7bh5
TitleXFEL structure of the ertapenem-derived CTX-M-15 acylenzyme after mixing for 2 sec 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/transpeptidase-like
Similarity search - Domain/homology
Chem-TVE / Beta-lactamase
Similarity search - Component
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)28,8294
Polymers28,2931
Non-polymers5363
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-21 kcal/mol
Surface area10780 Å2
Unit cell
Length a, b, c (Å)44.850, 45.493, 117.564
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-TVE / (2~{S},3~{R},4~{R})-3-[5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl]sulfanyl-4-methyl-5-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-2-carboxylic acid


Mass: 477.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27N3O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 41.97 %
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: 307 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.2399 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: 1.2399 Å / Relative weight: 1
ReflectionResolution: 1.55→58.78 Å / Num. obs: 35730 / % possible obs: 100 % / Redundancy: 134.23 % / Biso Wilson estimate: 22.37 Å2 / CC1/2: 0.961 / R split: 0.21 / Net I/σ(I): 39.566
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 48.45 % / Mean I/σ(I) obs: 0.71 / Num. unique obs: 1751 / CC1/2: 0.097 / R split: 1.232 / % possible all: 100
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
PHENIX1.18.2_3874refinement
cctbx.xfeldata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6qw8

6qw8


Resolution: 1.55→31.94 Å / SU ML: 0.2419 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.597
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2018 1783 5.01 %
Rwork0.1779 33834 -
obs0.1791 35617 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.62 Å2
Refinement stepCycle: LAST / Resolution: 1.55→31.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1943 0 18 143 2104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012028
X-RAY DIFFRACTIONf_angle_d1.07272760
X-RAY DIFFRACTIONf_chiral_restr0.0567324
X-RAY DIFFRACTIONf_plane_restr0.007363
X-RAY DIFFRACTIONf_dihedral_angle_d19.2993760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.40691280.42722509X-RAY DIFFRACTION97.41
1.59-1.640.49761240.40772518X-RAY DIFFRACTION97.63
1.64-1.690.35381640.3312528X-RAY DIFFRACTION99.93
1.69-1.750.29621710.24982548X-RAY DIFFRACTION100
1.75-1.820.27341510.22242570X-RAY DIFFRACTION100
1.82-1.910.22681120.20852596X-RAY DIFFRACTION99.96
1.91-2.010.24881450.18622581X-RAY DIFFRACTION100
2.01-2.130.19021270.1742619X-RAY DIFFRACTION100
2.13-2.30.21131300.16772595X-RAY DIFFRACTION100
2.3-2.530.19681270.16852640X-RAY DIFFRACTION100
2.53-2.890.20891290.16952643X-RAY DIFFRACTION100
2.89-3.640.14161120.15092681X-RAY DIFFRACTION100
3.64-31.940.16451630.14782806X-RAY DIFFRACTION100
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)
13.682467408913.36520557654-2.247612391397.74134982694-3.360976005815.8706077081-0.1584135254020.444404633976-0.541314244484-0.5206841334180.10651705101-0.6213955256460.2926160110060.09194094213220.07583429423680.2072936540690.0101555848070.01977342958790.254539552305-0.05789654632240.280775261485.20836422929-20.5742786924.08588975226
21.94594520354-0.597986288756-0.9353370229381.89111962340.3305057929111.1206537769-0.00750488843594-0.1961793073640.05342326878460.1611316479640.01733690004260.0584923733320.04357670982140.08428444663150.002349313346760.202641917429-0.0165479774101-0.0219367766920.2161066680880.002999624556080.168870084212-5.59263063328-11.51144486823.798717604
36.53414899773-2.0703956974-3.479055646325.670079397193.429258120592.98258597040.08970012825190.2278856015980.254305924313-0.479535437548-0.08275357607660.386353790389-0.450267720232-0.02153157506540.03765540930270.2569011245370.00806646864239-0.02967212664470.208139237760.03414638710760.274471462811-15.73274695877.926944460618.5427515529
46.46174430701-2.36408737161.217859132742.91683561961-0.3439204811580.70216376412-0.0121775002567-0.01969787296540.07037651151620.09000571252590.006681596840980.129747048126-0.00216336735707-0.01371667136150.008453999084060.170815466334-0.02359003331640.02247210859880.157551769602-0.002157096579350.139955797849-9.16092381109-3.1877796639325.6003523933
50.7914750398270.277938870982-0.01925641670421.083508776210.2927165447091.157993543250.0104380268774-0.00600083450348-0.00824072964283-0.00718707540660.0009569754361010.05128878132730.0302070365236-0.0317827849686-0.01189074670890.1766689246060.00732513850807-0.001945219649530.1608349259810.0024881981520.163295171777-5.01889805849-12.665897735417.5799539363
66.868858876294.29409105788-3.082281271373.3281121069-3.378164564493.93128028719-0.01434933983670.183994566222-0.191453028996-0.2968623259130.00701758848769-0.1583977535890.2117814837810.0663886661675-0.1413461208030.2152116827410.02589697609870.01801492459990.145042634727-0.0576961357360.122543322255-2.35623927708-14.80833519727.71838858788
74.77748563846-1.276851840190.6731850697683.48061078395-3.49226482013.60602093615-0.008367283218480.331391817048-0.0541710528983-0.5959002547220.1952228930860.1124733126420.29606206091-0.135949795034-0.1070352512790.271035513525-0.0152417129129-0.002471586433890.223946785785-0.02867786059440.158296675048-3.60871612941-19.61052476673.1521401537
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 28 through 51 )28 - 511 - 24
22chain 'A' and (resid 52 through 96 )52 - 9625 - 70
33chain 'A' and (resid 97 through 115 )97 - 11571 - 89
44chain 'A' and (resid 116 through 155 )116 - 15590 - 131
55chain 'A' and (resid 156 through 250 )156 - 250132 - 230
66chain 'A' and (resid 251 through 273 )251 - 273231 - 253
77chain 'A' and (resid 274 through 287 )274 - 287254 - 267

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