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- PDB-9oz5: Gradient equilibration of tetragonal lysozyme from 8% NaCl to 3% ... -

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Basic information

Entry
Database: PDB / ID: 9oz5
TitleGradient equilibration of tetragonal lysozyme from 8% NaCl to 3% NaCl over 40 minutes
ComponentsLysozyme C
KeywordsHYDROLASE / Glycosidase
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 / SAD / Resolution: 1.3 Å
AuthorsJuers, D.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM090248 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Automated gradient equilibration of macromolecular crystals to new solution conditions.
Authors: Juers, D.H. / Quire, J. / Stothers, S.
History
DepositionJun 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 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)14,4023
Polymers14,3311
Non-polymers712
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.182, 79.182, 37.985
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-335-

HOH

21A-338-

HOH

31A-398-

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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.08 Å3/Da / Density % sol: 40.79 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 8% NaCl, 20 mM NaOAc pH 5.2

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Data collection

DiffractionMean temperature: 294 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Jun 1, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.3→28 Å / Num. obs: 56713 / % possible obs: 100 % / Redundancy: 8.9 % / Biso Wilson estimate: 16.14 Å2 / CC1/2: 1 / Net I/σ(I): 20.9
Reflection shellResolution: 1.3→1.32 Å / Num. unique obs: 1460 / CC1/2: 0.354

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→28 Å / SU ML: 0.1658 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.8425
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1747 2866 5.05 %
Rwork0.1606 53847 -
obs0.1614 56713 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.72 Å2
Refinement stepCycle: LAST / Resolution: 1.3→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 2 98 1101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711071
X-RAY DIFFRACTIONf_angle_d0.90411459
X-RAY DIFFRACTIONf_chiral_restr0.078152
X-RAY DIFFRACTIONf_plane_restr0.0086194
X-RAY DIFFRACTIONf_dihedral_angle_d13.3948401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.320.35571470.33842644X-RAY DIFFRACTION99.29
1.32-1.350.30741470.31382682X-RAY DIFFRACTION99.65
1.35-1.370.27341310.30122714X-RAY DIFFRACTION99.86
1.37-1.40.3121150.28442708X-RAY DIFFRACTION99.89
1.4-1.430.31921670.2732662X-RAY DIFFRACTION100
1.43-1.460.26741600.25232723X-RAY DIFFRACTION100
1.46-1.50.231420.22912649X-RAY DIFFRACTION100
1.5-1.540.24741580.212690X-RAY DIFFRACTION99.96
1.54-1.590.23861310.19532725X-RAY DIFFRACTION100
1.59-1.640.18661290.18452685X-RAY DIFFRACTION100
1.64-1.70.21011610.18122686X-RAY DIFFRACTION100
1.7-1.760.2051310.17522714X-RAY DIFFRACTION100
1.76-1.840.16491530.17032658X-RAY DIFFRACTION100
1.84-1.940.19061240.15642734X-RAY DIFFRACTION100
1.94-2.060.16981300.14292704X-RAY DIFFRACTION100
2.06-2.220.17891600.13712680X-RAY DIFFRACTION100
2.22-2.450.14971490.13672695X-RAY DIFFRACTION100
2.45-2.80.18081440.15152684X-RAY DIFFRACTION100
2.8-3.530.15631450.1432708X-RAY DIFFRACTION100
3.53-280.12271420.12722702X-RAY DIFFRACTION99.89

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