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Basic information

Entry
Database: PDB / ID: 6web
TitleMulti-Hit SFX using MHz XFEL sources
ComponentsLysozyme
KeywordsHYDROLASE / Enzyme
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsHolmes, S. / Darmanin, C. / Abbey, B.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)CE140100011 Australia
Citation
Journal: Nat Commun / Year: 2022
Title: Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers.
Authors: Holmes, S. / Kirkwood, H.J. / Bean, R. / Giewekemeyer, K. / Martin, A.V. / Hadian-Jazi, M. / Wiedorn, M.O. / Oberthur, D. / Marman, H. / Adriano, L. / Al-Qudami, N. / Bajt, S. / Barak, I. / ...Authors: Holmes, S. / Kirkwood, H.J. / Bean, R. / Giewekemeyer, K. / Martin, A.V. / Hadian-Jazi, M. / Wiedorn, M.O. / Oberthur, D. / Marman, H. / Adriano, L. / Al-Qudami, N. / Bajt, S. / Barak, I. / Bari, S. / Bielecki, J. / Brockhauser, S. / Coleman, M.A. / Cruz-Mazo, F. / Danilevski, C. / Dorner, K. / Ganan-Calvo, A.M. / Graceffa, R. / Fanghor, H. / Heymann, M. / Frank, M. / Kaukher, A. / Kim, Y. / Kobe, B. / Knoska, J. / Laurus, T. / Letrun, R. / Maia, L. / Messerschmidt, M. / Metz, M. / Michelat, T. / Mills, G. / Molodtsov, S. / Monteiro, D.C.F. / Morgan, A.J. / Munnich, A. / Pena Murillo, G.E. / Previtali, G. / Round, A. / Sato, T. / Schubert, R. / Schulz, J. / Shelby, M. / Seuring, C. / Sellberg, J.A. / Sikorski, M. / Silenzi, A. / Stern, S. / Sztuk-Dambietz, J. / Szuba, J. / Trebbin, M. / Vagovic, P. / Ve, T. / Weinhausen, B. / Wrona, K. / Xavier, P.L. / Xu, C. / Yefanov, O. / Nugent, K.A. / Chapman, H.N. / Mancuso, A.P. / Barty, A. / Abbey, B. / Darmanin, C.
#1: Journal: 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.
#2: Journal: Struct Dyn. / Year: 2019
Title: Evaluation of serial crystallographic structure determination within megahertz pulse trains.
Authors: Yefanov, O. / Oberthur, D. / Bean, R. / Wiedorn, M.O. / Knoska, J. / Pena, G. / Awel, S. / Gumprecht, L. / Domaracky, M. / Sarrou, I. / Lourdu Xavier, P. / Metz, M. / Bajt, S. / Mariani, V. ...Authors: Yefanov, O. / Oberthur, D. / Bean, R. / Wiedorn, M.O. / Knoska, J. / Pena, G. / Awel, S. / Gumprecht, L. / Domaracky, M. / Sarrou, I. / Lourdu Xavier, P. / Metz, M. / Bajt, S. / Mariani, V. / Gevorkov, Y. / White, T.A. / Tolstikova, A. / Villanueva-Perez, P. / Seuring, C. / Aplin, S. / Estillore, A.D. / Kupper, J. / Klyuev, A. / Kuhn, M. / Laurus, T. / Graafsma, H. / Monteiro, D.C.F. / Trebbin, M. / Maia, F.R.N.C. / Cruz-Mazo, F. / Ganan-Calvo, A.M. / Heymann, M. / Darmanin, C. / Abbey, B. / Schmidt, M. / Fromme, P. / Giewekemeyer, K. / Sikorski, M. / Graceffa, R. / Vagovic, P. / Kluyver, T. / Bergemann, M. / Fangohr, H. / Sztuk-Dambietz, J. / Hauf, S. / Raab, N. / Bondar, V. / Mancuso, A.P. / Chapman, H. / Barty, A.
History
DepositionApr 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4884
Polymers14,3311
Non-polymers1573
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.300, 79.300, 37.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Lysozyme /


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: B8YK79, lysozyme
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.07 Å3/Da / Density % sol: 40.56 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 3.5
Details: NaCl, ethylene glycol, PEG 3350, acetate buffer pH 3.5

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: European XFEL / Beamline: SPB/SFX / Wavelength: 1.3332 Å
DetectorType: AGIPD / Detector: PIXEL / Date: Sep 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3332 Å / Relative weight: 1
ReflectionResolution: 2.1→21.66 Å / Num. obs: 7448 / % possible obs: 99.9 % / Redundancy: 1 % / CC1/2: 0.906 / Net I/σ(I): 5.1
Reflection shellResolution: 2.1→2.155 Å / Num. unique obs: 535 / CC1/2: 0.787 / % possible all: 100
Serial crystallography sample deliveryMethod: injection

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.65 Å21.65 Å

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHASER2.8.3phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
Cheetahdata collection
Cootmodel building
CrystFELdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FTR

6ftr


Resolution: 2.1→21.66 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.909 / SU B: 9.646 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R Free: 0.188
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2163 737 9.9 %RANDOM
Rwork0.152 ---
obs0.1585 6681 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 68.03 Å2 / Biso mean: 19.575 Å2 / Biso min: 10.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.27 Å2
Refinement stepCycle: final / Resolution: 2.1→21.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 9 51 1060
Biso mean--36.09 29.96 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131037
X-RAY DIFFRACTIONr_bond_other_d0.0010.018924
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.6361401
X-RAY DIFFRACTIONr_angle_other_deg1.3831.592134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2075129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.87920.65661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52715170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1581511
X-RAY DIFFRACTIONr_chiral_restr0.0770.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021187
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02246
X-RAY DIFFRACTIONr_rigid_bond_restr1.39531960
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1550.183560.114479X-RAY DIFFRACTION100
2.155-2.2140.218560.12519X-RAY DIFFRACTION100
2.214-2.2780.296480.124501X-RAY DIFFRACTION100
2.278-2.3480.263460.12499X-RAY DIFFRACTION100
2.348-2.4250.19320.127474X-RAY DIFFRACTION100

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