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- PDB-6qy2: Pink beam serial crystallography: Lysozyme, 5 us exposure, 750 pa... -

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Basic information

Entry
Database: PDB / ID: 6qy2
TitlePink beam serial crystallography: Lysozyme, 5 us exposure, 750 patterns merged
ComponentsLysozyme C
KeywordsHYDROLASE / pink beam / fixed-target / serial crystallography / lysozyme
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
Lysozyme - #10 / 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 / Lysozyme-like domain superfamily ...Lysozyme - #10 / 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 / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLieske, J. / Tolstikova, A. / Meents, A.
Funding support Germany, 5items
OrganizationGrant numberCountry
European Commission637295
German Federal Ministry for Education and Research031B0405D Germany
European Union654220
European Research Council609920
German Federal Ministry for Education and Research05K2018-201-06727 MXD Germany
CitationJournal: Iucrj / Year: 2019
Title: 1 kHz fixed-target serial crystallography using a multilayer monochromator and an integrating pixel detector.
Authors: Tolstikova, A. / Levantino, M. / Yefanov, O. / Hennicke, V. / Fischer, P. / Meyer, J. / Mozzanica, A. / Redford, S. / Crosas, E. / Opara, N.L. / Barthelmess, M. / Lieske, J. / Oberthuer, D. ...Authors: Tolstikova, A. / Levantino, M. / Yefanov, O. / Hennicke, V. / Fischer, P. / Meyer, J. / Mozzanica, A. / Redford, S. / Crosas, E. / Opara, N.L. / Barthelmess, M. / Lieske, J. / Oberthuer, D. / Wator, E. / Mohacsi, I. / Wulff, M. / Schmitt, B. / Chapman, H.N. / Meents, A.
History
DepositionMar 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: 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 1.2Jan 24, 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5106
Polymers14,3311
Non-polymers1795
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-36 kcal/mol
Surface area6600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.860, 79.860, 38.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-343-

HOH

21A-357-

HOH

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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 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 50mM sodium acetate 3.5, 0.75M sodium chloride, 30% ethylene glycol, 11.25% polyethylene glycol 400

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 0.8058-0.8262
DetectorType: PSI JUNGFRAU 1M / Detector: PIXEL / Date: Jul 15, 2017
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.80581
20.82621
ReflectionResolution: 1.7→27.535 Å / Num. obs: 11637 / % possible obs: 82 % / Redundancy: 11.4 % / Net I/σ(I): 3.84
Reflection shellResolution: 1.7→1.761 Å / CC1/2: 0.7996
Serial crystallography sample deliveryDescription: Roadrunner II / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: Roadrunner II

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155_9999refinement
PDB_EXTRACT3.24data extraction
CrystFEL0.6.3data reduction
CrystFEL0.8.0data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FTR

6ftr


Resolution: 1.7→27.535 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26
RfactorNum. reflection% reflection
Rfree0.2417 1138 9.84 %
Rwork0.2152 --
obs0.2179 11569 82.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 65.71 Å2 / Biso mean: 25.8791 Å2 / Biso min: 9.3 Å2
Refinement stepCycle: final / Resolution: 1.7→27.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 14 81 1096
Biso mean--32.13 33.26 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021114
X-RAY DIFFRACTIONf_angle_d0.5561521
X-RAY DIFFRACTIONf_chiral_restr0.039157
X-RAY DIFFRACTIONf_plane_restr0.003202
X-RAY DIFFRACTIONf_dihedral_angle_d10.474690
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.77740.3182270.32229832519
1.7774-1.87110.30431000.283888098057
1.8711-1.98830.29341410.25131298143983
1.9883-2.14170.2461650.21931508167397
2.1417-2.35720.21591710.196315641735100
2.3572-2.6980.22551750.193615861761100
2.698-3.39820.24521720.200616031775100
3.3982-27.53830.23761870.220816941881100

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