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- PDB-9fud: Serial microseconds crystallography at ID29 using fixed-target (S... -

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Basic information

Entry
Database: PDB / ID: 9fud
TitleSerial microseconds crystallography at ID29 using fixed-target (Si Chip): Lysozyme - without ligand GlcNAc (apo)
ComponentsLysozyme C
KeywordsHYDROLASE / Serial crystallography / serial microsecond crystallography / room temperature / ID29 / ESRF-EBS / fixed-target / lysozyme / apo
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsOrlans, J. / Rose, S.L. / Basu, S. / de Sanctis, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Chem / Year: 2025
Title: Advancing macromolecular structure determination with microsecond X-ray pulses at a 4th generation synchrotron.
Authors: Orlans, J. / Rose, S.L. / Ferguson, G. / Oscarsson, M. / Homs Puron, A. / Beteva, A. / Debionne, S. / Theveneau, P. / Coquelle, N. / Kieffer, J. / Busca, P. / Sinoir, J. / Armijo, V. / Lopez ...Authors: Orlans, J. / Rose, S.L. / Ferguson, G. / Oscarsson, M. / Homs Puron, A. / Beteva, A. / Debionne, S. / Theveneau, P. / Coquelle, N. / Kieffer, J. / Busca, P. / Sinoir, J. / Armijo, V. / Lopez Marrero, M. / Felisaz, F. / Papp, G. / Gonzalez, H. / Caserotto, H. / Dobias, F. / Gigmes, J. / Lebon, G. / Basu, S. / de Sanctis, D.
History
DepositionJun 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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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)14,4966
Polymers14,3311
Non-polymers1655
Water64936
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-51 kcal/mol
Surface area6270 Å2
Unit cell
Length a, b, c (Å)78.700, 78.700, 37.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-328-

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.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.05 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 3
Details: 1 M sodium acetate pH 3.0, 20% (w/v) NaCl, 5% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å
DetectorType: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Mar 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.05→55.65 Å / Num. obs: 7923 / % possible obs: 100 % / Redundancy: 101 % / Biso Wilson estimate: 46.25 Å2 / CC star: 0.9958 / R split: 0.163 / Net I/σ(I): 4.16
Reflection shellResolution: 2.05→2.08 Å / Num. unique obs: 323 / CC star: 0.3695 / R split: 2.5695
Serial crystallography sample deliveryDescription: Si chip / Method: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→55.65 Å / SU ML: 0.3141 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.2079
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2523 782 10.04 %
Rwork0.216 7005 -
obs0.2197 7787 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.15 Å2
Refinement stepCycle: LAST / Resolution: 2.05→55.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms964 0 5 36 1005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029999
X-RAY DIFFRACTIONf_angle_d0.49051361
X-RAY DIFFRACTIONf_chiral_restr0.0411146
X-RAY DIFFRACTIONf_plane_restr0.0033179
X-RAY DIFFRACTIONf_dihedral_angle_d12.4373344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.180.39051220.37341061X-RAY DIFFRACTION92.06
2.18-2.350.39681280.3271152X-RAY DIFFRACTION99.92
2.35-2.580.30541280.28431155X-RAY DIFFRACTION100
2.58-2.960.29811300.26241176X-RAY DIFFRACTION100
2.96-3.720.23991320.19711186X-RAY DIFFRACTION100
3.73-55.650.20721420.17421275X-RAY DIFFRACTION100

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