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Basic information

Entry
Database: PDB / ID: 7tum
TitleMulti-Hit SFX using MHz XFEL sources- first hit
ComponentsLysozyme C
KeywordsHYDROLASE / Enzyme
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / 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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3.202 Å
AuthorsDarmanin, C. / Holmes, S. / Abbey, B.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)CE140100011 Australia
CitationJournal: 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.
History
DepositionFeb 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2022Provider: 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
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

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4163
Polymers14,3311
Non-polymers852
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 1 / Fragment: lyzozyme
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.2→35.49 Å / Num. obs: 2072 / % possible obs: 93.6 % / Redundancy: 4.55 % / CC1/2: 0.412 / CC star: 0.764 / Net I/σ(I): 4.36
Reflection shellResolution: 3.2→3.28 Å / Num. unique obs: 403 / CC1/2: 0.638 / CC star: 0.882 / % possible all: 90.79
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionDescription: GDVN

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
CrystFELdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FTR

6ftr


Resolution: 3.202→35.489 Å / Cor.coef. Fo:Fc: 0.782 / Cor.coef. Fo:Fc free: 0.577 / WRfactor Rfree: 0.666 / WRfactor Rwork: 0.394 / SU B: 124.233 / SU ML: 1.002 / Average fsc free: 0.7065 / Average fsc work: 0.7911 / Cross valid method: FREE R-VALUE / ESU R Free: 1.098
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.4262 207 10.063 %
Rwork0.3138 1850 -
all0.325 --
obs-2057 93.585 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 10.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.374 Å20 Å20 Å2
2---0.374 Å20 Å2
3---0.748 Å2
Refinement stepCycle: LAST / Resolution: 3.202→35.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 5 3 1009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0131091
X-RAY DIFFRACTIONr_bond_other_d0.0050.018961
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.6371486
X-RAY DIFFRACTIONr_angle_other_deg1.2231.5882219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5695141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65720.29967
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.78215176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2371513
X-RAY DIFFRACTIONr_chiral_restr0.0630.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021302
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02269
X-RAY DIFFRACTIONr_nbd_refined0.2210.2296
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2160.21017
X-RAY DIFFRACTIONr_nbtor_refined0.160.2504
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.2467
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.224
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0370.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2260.217
X-RAY DIFFRACTIONr_nbd_other0.3170.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2740.28
X-RAY DIFFRACTIONr_mcbond_it0.4030.814550
X-RAY DIFFRACTIONr_mcbond_other0.390.813549
X-RAY DIFFRACTIONr_mcangle_it0.5811.219697
X-RAY DIFFRACTIONr_mcangle_other0.5821.22698
X-RAY DIFFRACTIONr_scbond_it0.3580.872540
X-RAY DIFFRACTIONr_scbond_other0.360.876541
X-RAY DIFFRACTIONr_scangle_it0.5011.293789
X-RAY DIFFRACTIONr_scangle_other0.5011.297790
X-RAY DIFFRACTIONr_lrange_it0.8899.7641312
X-RAY DIFFRACTIONr_lrange_other0.8899.7831313
X-RAY DIFFRACTIONr_rigid_bond_restr1.16632046
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.202-3.2850.40690.323129X-RAY DIFFRACTION90.7895
3.285-3.3750.374170.289125X-RAY DIFFRACTION92.2078
3.375-3.4720.495180.28120X-RAY DIFFRACTION93.2432
3.472-3.5790.426110.264115X-RAY DIFFRACTION91.9708
3.579-3.6960.429170.3116X-RAY DIFFRACTION91.7241
3.696-3.8250.522110.272112X-RAY DIFFRACTION89.781
3.825-3.9690.46260.307122X-RAY DIFFRACTION95.5224
3.969-4.1310.15760.238101X-RAY DIFFRACTION86.9919
4.131-4.3140.239140.311100X-RAY DIFFRACTION92.6829
4.314-4.5240.35100.29100X-RAY DIFFRACTION93.2203
4.524-4.7680.623130.34399X-RAY DIFFRACTION94.9153
4.768-5.0560.431140.3684X-RAY DIFFRACTION95.1456
5.056-5.4040.62370.31199X-RAY DIFFRACTION97.2477
5.404-5.8340.68980.31581X-RAY DIFFRACTION94.6809
5.834-6.3880.387110.37977X-RAY DIFFRACTION98.8764
6.388-7.1360.678120.3867X-RAY DIFFRACTION96.3415
7.136-8.2290.43270.38763X-RAY DIFFRACTION95.8904
8.229-10.0510.34290.33662X-RAY DIFFRACTION100
10.051-14.1020.41140.39948X-RAY DIFFRACTION100
14.102-35.4890.35630.43730X-RAY DIFFRACTION91.6667
Refinement TLS params.Method: refined / Origin x: 0.7459 Å / Origin y: 99.8512 Å / Origin z: 9.2205 Å
111213212223313233
T0.0077 Å2-0.0042 Å20.007 Å2-0.0063 Å20.0033 Å2--0.0233 Å2
L0.4679 °20.2475 °2-0.3796 °2-0.6246 °20.3701 °2--0.9689 °2
S-0.0048 Å °-0.0341 Å °-0.0534 Å °-0.0644 Å °0.0198 Å °-0.0819 Å °-0.0662 Å °0.0711 Å °-0.015 Å °
Refinement TLS groupSelection: ALL

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