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- PDB-45kk: 6-conformation model of Hen Egg White Lysozyme at 100K -

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Basic information

Entry
Database: PDB / ID: 45kk
Title6-conformation model of Hen Egg White Lysozyme at 100K
ComponentsLysozyme C
KeywordsISOMERASE / 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 / 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 / Golgi apparatus / endoplasmic reticulum / extracellular region / 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
ACETATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsPassmore, S.K.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT220100405 Australia
Citation
Journal: Biorxiv / Year: 2026
Title: Optimizing the connectivity of protein conformations to untangle ensemble refinement
Authors: Passmore, S.K. / Holton, J.M. / Zatsepin, N.A. / Martin, A.V.
#1: Journal: J.Synchrotron Radiat. / Year: 2017
Title: Conformational variation of proteins at room temperature is not dominated by radiation damage.
Authors: Russi, S. / Gonzalez, A. / Kenner, L.R. / Keedy, D.A. / Fraser, J.S. / van den Bedem, H.
History
DepositionSep 1, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Remark 0THIS ENTRY 45KK REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 5KXK, DETERMINED BY S. ...THIS ENTRY 45KK REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 5KXK, DETERMINED BY S.Russi, A.Gonzalez, L.R.Kenner, D.A.Keedy, J.S.Fraser, H.van den Bedem.

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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)14,5437
Polymers14,3311
Non-polymers2116
Water26,4461468
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-37 kcal/mol
Surface area6520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.289, 77.289, 37.205
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-129-

LEU

21A-129-

LEU

31A-438-

HOH

41A-817-

HOH

51A-1009-

HOH

61A-1416-

HOH

71A-1541-

HOH

81A-1573-

HOH

91A-1668-

HOH

101A-1688-

HOH

111A-1718-

HOH

121A-1751-

HOH

131A-1752-

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 genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NA / SODIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 1468 / 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: 1.94 Å3/Da / Density % sol: 36.55 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 5KXK
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (1.0 M SODIUM CHLORIDE, 50 MM SODIUM ACETATE PH 4.5) AND PROTEIN (40-60 MG/ML)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.21549 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 19, 2013
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.21549 Å / Relative weight: 1
ReflectionResolution: 1.198→38.65 Å / Num. obs: 35966 / % possible obs: 99.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 9.29 Å2 / Rsym value: 0.025 / Net I/σ(I): 45.8
Reflection shellResolution: 1.2→1.26 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 8 / Num. unique obs: 4943 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX2.0_5793refinement
XDSdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→38.64 Å / SU ML: 0.0477 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 5.7449
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Model was refined over loops consisting of a single unrestrained refinement macro-cycle, connectivity optimization (reassigning altloc labels), then 10+ restrained refinement macro-cycles. ...Details: Model was refined over loops consisting of a single unrestrained refinement macro-cycle, connectivity optimization (reassigning altloc labels), then 10+ restrained refinement macro-cycles. Conformation-aware water picking and manual adjustments were also performed in later loops.
RfactorNum. reflection% reflection
Rfree0.0853 1998 5.56 %
Rwork0.0503 33955 -
obs0.0522 35953 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 8.93 Å2
Refinement stepCycle: LAST / Resolution: 1.2→38.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 9 1468 2478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00896168
X-RAY DIFFRACTIONf_angle_d1.05968352
X-RAY DIFFRACTIONf_chiral_restr0.0881864
X-RAY DIFFRACTIONf_plane_restr0.01351092
X-RAY DIFFRACTIONf_dihedral_angle_d13.41422190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.230.08931390.05072374X-RAY DIFFRACTION99.33
1.23-1.260.10371410.04732381X-RAY DIFFRACTION100
1.26-1.30.10161400.04592380X-RAY DIFFRACTION100
1.3-1.340.08881410.04362399X-RAY DIFFRACTION100
1.34-1.390.09221400.04532378X-RAY DIFFRACTION100
1.39-1.440.09651420.04262400X-RAY DIFFRACTION100
1.44-1.510.08791400.04222399X-RAY DIFFRACTION100
1.51-1.590.08751430.0462408X-RAY DIFFRACTION100
1.59-1.690.09471420.04782428X-RAY DIFFRACTION100
1.69-1.820.10011420.04962411X-RAY DIFFRACTION100
1.82-20.07931440.0482438X-RAY DIFFRACTION100
2-2.290.08321440.04582453X-RAY DIFFRACTION100
2.29-2.890.07391470.0532501X-RAY DIFFRACTION100
2.89-38.640.08121530.05822605X-RAY DIFFRACTION99.53

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