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- PDB-8cl5: Lysozyme in matrix of lipidic cubic phase of monoolein (LCP) -

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Basic information

Entry
Database: PDB / ID: 8cl5
TitleLysozyme in matrix of lipidic cubic phase of monoolein (LCP)
ComponentsLYSOZYME, Chain A
KeywordsHYDROLASE / lysozyme / lysozyme activity / catalytic activity / hydrolase activity
Biological speciesAsplenium bulbiferum subsp. bulbiferum (hen and chickens fern)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsBertrand, Q. / Kepa, M.W. / Weinert, T. / Wranik, M. / Standfuss, J.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_179351 Switzerland
Swiss National Science Foundation310030_207462 Switzerland
Swiss National Science Foundation310030_192566 Switzerland
CitationJournal: Nat Commun / Year: 2023
Title: A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers.
Authors: Wranik, M. / Kepa, M.W. / Beale, E.V. / James, D. / Bertrand, Q. / Weinert, T. / Furrer, A. / Glover, H. / Gashi, D. / Carrillo, M. / Kondo, Y. / Stipp, R.T. / Khusainov, G. / Nass, K. / ...Authors: Wranik, M. / Kepa, M.W. / Beale, E.V. / James, D. / Bertrand, Q. / Weinert, T. / Furrer, A. / Glover, H. / Gashi, D. / Carrillo, M. / Kondo, Y. / Stipp, R.T. / Khusainov, G. / Nass, K. / Ozerov, D. / Cirelli, C. / Johnson, P.J.M. / Dworkowski, F. / Beale, J.H. / Stubbs, S. / Zamofing, T. / Schneider, M. / Krauskopf, K. / Gao, L. / Thorn-Seshold, O. / Bostedt, C. / Bacellar, C. / Steinmetz, M.O. / Milne, C. / Standfuss, J.
History
DepositionFeb 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LYSOZYME, Chain A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7487
Polymers14,3311
Non-polymers4176
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-26 kcal/mol
Surface area6410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.920, 77.920, 37.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-323-

HOH

21A-334-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LYSOZYME, Chain A


Mass: 14331.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Asplenium bulbiferum subsp. bulbiferum (hen and chickens fern)
Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 120 molecules

#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.99 Å3/Da / Density % sol: 38.29 %
Crystal growTemperature: 295 K / Method: batch mode / pH: 3
Details: 25 mg/mL, 100 mM sodium acetate, lysozyme solution added to 28% (w/v) sodium chloride, 8% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 1.03 Å
DetectorType: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Feb 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.31→14.995 Å / Num. obs: 26527 / % possible obs: 99.85 % / Redundancy: 423.46 % / CC1/2: 0.975 / Net I/σ(I): 7.31
Reflection shellResolution: 1.31→1.36 Å / Num. unique obs: 1466 / CC1/2: 0.204 / % possible all: 98.59
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
CrystFEL0.9.1data reduction
CrystFEL0.9.1data scaling
PHASER1.20_4459phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.31→14.47 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1479 1999 7.54 %
Rwork0.1246 --
obs0.1264 26527 92.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.31→14.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 16 114 1131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016
X-RAY DIFFRACTIONf_angle_d1.421
X-RAY DIFFRACTIONf_dihedral_angle_d14.349476
X-RAY DIFFRACTIONf_chiral_restr0.108166
X-RAY DIFFRACTIONf_plane_restr0.011234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.340.3714260.4185320X-RAY DIFFRACTION17
1.34-1.370.31961170.30521435X-RAY DIFFRACTION77
1.37-1.410.29411490.21111824X-RAY DIFFRACTION98
1.41-1.460.19051500.14561846X-RAY DIFFRACTION100
1.46-1.510.14681520.111869X-RAY DIFFRACTION100
1.51-1.570.13441550.10381886X-RAY DIFFRACTION100
1.57-1.640.14771520.10591871X-RAY DIFFRACTION100
1.64-1.730.13491540.09821891X-RAY DIFFRACTION100
1.73-1.840.1371530.09781876X-RAY DIFFRACTION100
1.84-1.980.1121540.09881903X-RAY DIFFRACTION100
1.98-2.180.13861540.10371886X-RAY DIFFRACTION100
2.18-2.490.1421580.11551925X-RAY DIFFRACTION100
2.49-3.140.13881590.13371951X-RAY DIFFRACTION100
3.14-14.470.15311660.13412045X-RAY DIFFRACTION100

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