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- PDB-9tot: Fixed target room temperature serial crystal structure of hen egg... -

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Basic information

Entry
Database: PDB / ID: 9tot
TitleFixed target room temperature serial crystal structure of hen egg white lysozyme at DLS I24, 600 s mix with N-acetyl glucosamine.
ComponentsLysozyme C
KeywordsHYDROLASE / lysozyme / serial / room temperature
Function / homology
Function and homology information


Lactose synthesis / 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 bacterium ...Lactose synthesis / 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 bacterium / defense response to Gram-positive bacterium / endoplasmic reticulum / : / 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
2-acetamido-2-deoxy-alpha-D-glucopyranose / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.64 Å
AuthorsHinchliffe, P. / Kamps, J.A.G. / Aller, P. / Orville, A.M.
Funding support United Kingdom, European Union, 4items
OrganizationGrant numberCountry
Wellcome Trust210734/Z/18/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/P007295/1 United Kingdom
European Research Council (ERC)101021207European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T008741/1 United Kingdom
CitationJournal: Iucrj / Year: 2026
Title: Drop-on-fixed-target reaction initiation approach for serial and time-resolved crystallography.
Authors: Kamps, J.J.A.G. / Hinchliffe, P. / Glerup, J. / Freeman, E.I. / Lang, P.A. / Tooke, C.L. / Beer, M. / Parkinson, L. / Gu, D.H. / Park, S. / Devenish, N. / Zhou, T. / Shilova, A. / Kaur, S. / ...Authors: Kamps, J.J.A.G. / Hinchliffe, P. / Glerup, J. / Freeman, E.I. / Lang, P.A. / Tooke, C.L. / Beer, M. / Parkinson, L. / Gu, D.H. / Park, S. / Devenish, N. / Zhou, T. / Shilova, A. / Kaur, S. / Rabe, P. / Schofield, C.J. / Spencer, J. / Park, J. / Owen, R.L. / Orville, A.M. / Aller, P.
History
DepositionDec 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release

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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)14,7177
Polymers14,3311
Non-polymers3866
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.164, 79.164, 38.113
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-340-

HOH

21A-359-

HOH

31A-390-

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: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-CL / CHLORIDE ION


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


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


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.08 Å3/Da / Density % sol: 40.96 %
Crystal growTemperature: 295 K / Method: batch mode
Details: 1 M citric acid, 20% (w/v) NaCl, 5% (w/v) PEG 6000, pH 3.0.

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9998 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 18, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.64→55.98 Å / Num. obs: 15382 / % possible obs: 100 % / Redundancy: 434.56 % / CC1/2: 0.056 / R split: 0.04 / Net I/σ(I): 7.597
Reflection shellResolution: 1.64→1.6683 Å / Redundancy: 203.2 % / Mean I/σ(I) obs: 0.835 / Num. unique obs: 760 / CC1/2: 0.388 / R split: 0.323 / % possible all: 100
Serial crystallography sample deliveryDescription: silicon 'Oxford' chip / Method: fixed target
Serial crystallography data reductionLattices indexed: 33400

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.64→55.98 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.187 769 5 %
Rwork0.1566 --
obs0.1581 15366 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.64→55.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms994 0 20 90 1104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051122
X-RAY DIFFRACTIONf_angle_d0.7881531
X-RAY DIFFRACTIONf_dihedral_angle_d12.608415
X-RAY DIFFRACTIONf_chiral_restr0.049162
X-RAY DIFFRACTIONf_plane_restr0.004203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.770.27771490.23212840X-RAY DIFFRACTION100
1.77-1.940.23851500.18232862X-RAY DIFFRACTION100
1.94-2.230.20231530.14932884X-RAY DIFFRACTION100
2.23-2.80.18471540.16872927X-RAY DIFFRACTION100
2.8-55.980.16751630.14113084X-RAY DIFFRACTION100

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