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- PDB-7bh3: XFEL structure of CTX-M-15 resting state -

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Basic information

Entry
Database: PDB / ID: 7bh3
TitleXFEL structure of CTX-M-15 resting state
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: 1.6 Å
AuthorsHinchliffe, P. / Tooke, C.L. / Butryn, A. / Spencer, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) 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

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4253
Polymers28,2931
Non-polymers1322
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-22 kcal/mol
Surface area10900 Å2
Unit cell
Length a, b, c (Å)44.886, 45.601, 117.572
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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 42.16 %
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: 1.2404 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: 1.2404 Å / Relative weight: 1
ReflectionResolution: 1.6→58.79 Å / Num. obs: 32656 / % possible obs: 100 % / Redundancy: 26.45 % / Biso Wilson estimate: 22.02 Å2 / CC1/2: 0.833 / R split: 0.441 / Net I/σ(I): 18.484
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 0.45 / Num. unique obs: 1585 / CC1/2: 0.02 / R split: 1.378 / % 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 / 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: 1.6→31.99 Å / SU ML: 0.3482 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.23
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2964 1602 4.95 %
Rwork0.246 30760 -
obs0.2485 32362 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.87 Å2
Refinement stepCycle: LAST / Resolution: 1.6→31.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 6 145 2103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01092044
X-RAY DIFFRACTIONf_angle_d1.12352784
X-RAY DIFFRACTIONf_chiral_restr0.0563323
X-RAY DIFFRACTIONf_plane_restr0.0085369
X-RAY DIFFRACTIONf_dihedral_angle_d21.3616771
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.650.50081210.44232533X-RAY DIFFRACTION91.45
1.65-1.710.3651450.36972736X-RAY DIFFRACTION99.24
1.71-1.780.40191500.34252784X-RAY DIFFRACTION99.73
1.78-1.860.35081480.34162775X-RAY DIFFRACTION99.83
1.86-1.960.36491580.32092781X-RAY DIFFRACTION99.8
1.96-2.080.36431510.29862773X-RAY DIFFRACTION99.93
2.08-2.240.34641340.28132822X-RAY DIFFRACTION99.9
2.24-2.470.31871570.27512821X-RAY DIFFRACTION99.97
2.47-2.820.32791360.25532844X-RAY DIFFRACTION99.97
2.82-3.560.28691520.21352868X-RAY DIFFRACTION99.97
3.56-31.990.20271500.17563023X-RAY DIFFRACTION99.97

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