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- PDB-6gth: Serial Femtosecond Crystallography at Megahertz pulse rates -

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Basic information

Entry
Database: PDB / ID: 6gth
TitleSerial Femtosecond Crystallography at Megahertz pulse rates
ComponentsBeta-lactamase
KeywordsANTIBIOTIC / Ser-beta-lactamase / inhibitor / complex / avibactam
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NXL / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsWiedorn, M. / Oberthuer, D. / Werner, N. / Schubert, R. / White, T.A. / Mancuso, A. / Perbandt, M. / Betzel, C. / Barty, A. / Chapman, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationCluster of Excellence 1074 Germany
CitationJournal: Nat Commun / Year: 2018
Title: Megahertz serial crystallography.
Authors: Wiedorn, M.O. / Oberthur, D. / Bean, R. / Schubert, R. / Werner, N. / Abbey, B. / Aepfelbacher, M. / Adriano, L. / Allahgholi, A. / Al-Qudami, N. / Andreasson, J. / Aplin, S. / Awel, S. / ...Authors: Wiedorn, M.O. / Oberthur, D. / Bean, R. / Schubert, R. / Werner, N. / Abbey, B. / Aepfelbacher, M. / Adriano, L. / Allahgholi, A. / Al-Qudami, N. / Andreasson, J. / Aplin, S. / Awel, S. / Ayyer, K. / Bajt, S. / Barak, I. / Bari, S. / Bielecki, J. / Botha, S. / Boukhelef, D. / Brehm, W. / Brockhauser, S. / Cheviakov, I. / Coleman, M.A. / Cruz-Mazo, F. / Danilevski, C. / Darmanin, C. / Doak, R.B. / Domaracky, M. / Dorner, K. / Du, Y. / Fangohr, H. / Fleckenstein, H. / Frank, M. / Fromme, P. / Ganan-Calvo, A.M. / Gevorkov, Y. / Giewekemeyer, K. / Ginn, H.M. / Graafsma, H. / Graceffa, R. / Greiffenberg, D. / Gumprecht, L. / Gottlicher, P. / Hajdu, J. / Hauf, S. / Heymann, M. / Holmes, S. / Horke, D.A. / Hunter, M.S. / Imlau, S. / Kaukher, A. / Kim, Y. / Klyuev, A. / Knoska, J. / Kobe, B. / Kuhn, M. / Kupitz, C. / Kupper, J. / Lahey-Rudolph, J.M. / Laurus, T. / Le Cong, K. / Letrun, R. / Xavier, P.L. / Maia, L. / Maia, F.R.N.C. / Mariani, V. / Messerschmidt, M. / Metz, M. / Mezza, D. / Michelat, T. / Mills, G. / Monteiro, D.C.F. / Morgan, A. / Muhlig, K. / Munke, A. / Munnich, A. / Nette, J. / Nugent, K.A. / Nuguid, T. / Orville, A.M. / Pandey, S. / Pena, G. / Villanueva-Perez, P. / Poehlsen, J. / Previtali, G. / Redecke, L. / Riekehr, W.M. / Rohde, H. / Round, A. / Safenreiter, T. / Sarrou, I. / Sato, T. / Schmidt, M. / Schmitt, B. / Schonherr, R. / Schulz, J. / Sellberg, J.A. / Seibert, M.M. / Seuring, C. / Shelby, M.L. / Shoeman, R.L. / Sikorski, M. / Silenzi, A. / Stan, C.A. / Shi, X. / Stern, S. / Sztuk-Dambietz, J. / Szuba, J. / Tolstikova, A. / Trebbin, M. / Trunk, U. / Vagovic, P. / Ve, T. / Weinhausen, B. / White, T.A. / Wrona, K. / Xu, C. / Yefanov, O. / Zatsepin, N. / Zhang, J. / Perbandt, M. / Mancuso, A.P. / Betzel, C. / Chapman, H. / Barty, A.
History
DepositionJun 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 14, 2018Group: Data collection / Structure summary / Category: diffrn / entity
Item: _diffrn.pdbx_serial_crystal_experiment / _entity.formula_weight
Revision 1.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)27,9252
Polymers27,6581
Non-polymers2671
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.840, 41.840, 233.280
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Beta-lactamase /


Mass: 27658.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ctx-m-14 / Production host: Escherichia coli (E. coli)
References: UniProt: D2D9A0, UniProt: A0A0H3H219*PLUS, beta-lactamase
#2: Chemical ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form / Avibactam


Mass: 267.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13N3O6S / Comment: antibiotic, inhibitor*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

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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: 42.29 %
Crystal growTemperature: 293 K / Method: batch mode
Details: CTX-M-14 microcrystals for SFX were produced using a seeding approach. Crystals were grown by sitting drop vapor diffusion at 290 overnight mixing 1 microliter CTX-M-14 at 20 mg ml-1 and 1 ...Details: CTX-M-14 microcrystals for SFX were produced using a seeding approach. Crystals were grown by sitting drop vapor diffusion at 290 overnight mixing 1 microliter CTX-M-14 at 20 mg ml-1 and 1 microliter precipitant (40 % PEG8000, 200 mM lithium sulfate, 100 mM sodium acetate). Obtained crystals (space group P212121) were crushed and a seed stock was prepared. To obtain microcrystals the undiluted seedstock was used for batch crystallization setups by mixing volumes of 50 % CTX-M-14 with 10 % undiluted seed stock and 40 % precipitant solution.

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Data collection

DiffractionMean temperature: 290 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: European XFEL / Beamline: SPB/SFX / Wavelength: 1.33 Å
DetectorType: AGIPD / Detector: PIXEL / Date: Apr 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.33 Å / Relative weight: 1
ReflectionResolution: 1.69→34.603 Å / Num. obs: 27838 / % possible obs: 99.89 % / Redundancy: 65.99 % / R split: 0.197 / Net I/σ(I): 4.37
Reflection shellResolution: 1.69→1.75 Å / R split: 0.476

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.24data extraction
CrystFELdata reduction
CrystFEL0.6.3data scaling
PHASERphasing
Cheetahdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TWD

5twd


Resolution: 1.69→34.603 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.48
RfactorNum. reflection% reflection
Rfree0.2096 2037 7.32 %
Rwork0.176 --
obs0.1785 27838 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 68.87 Å2 / Biso mean: 25.55 Å2 / Biso min: 11.12 Å2
Refinement stepCycle: final / Resolution: 1.69→34.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 28 200 2169
Biso mean--22.24 36.62 -
Num. residues----260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082020
X-RAY DIFFRACTIONf_angle_d1.2232756
X-RAY DIFFRACTIONf_chiral_restr0.043326
X-RAY DIFFRACTIONf_plane_restr0.006362
X-RAY DIFFRACTIONf_dihedral_angle_d12.307743
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.69-1.72930.2961310.271688181999
1.7293-1.77260.27771320.225116421774100
1.7726-1.82050.25571360.211817201856100
1.8205-1.87410.27641300.200216401770100
1.8741-1.93460.24821330.195117031836100
1.9346-2.00370.2461340.1717031837100
2.0037-2.08390.2131320.169316981830100
2.0839-2.17880.19241340.166116891823100
2.1788-2.29360.19541300.164717021832100
2.2936-2.43730.23951370.166317191856100
2.4373-2.62540.2451380.169817271865100
2.6254-2.88950.2181390.177217071846100
2.8895-3.30730.21341410.179317611902100
3.3073-4.16570.18261410.157717981939100
4.1657-34.61050.17251490.181719042053100

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