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- PDB-9p12: Lysozyme Room-Temperature In-Situ, Shipped -

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Basic information

Entry
Database: PDB / ID: 9p12
TitleLysozyme Room-Temperature In-Situ, Shipped
ComponentsLysozyme C
KeywordsHYDROLASE
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: 1.57 Å
AuthorsSnell, M.E. / Campomizzi, C.S. / Mikolajek, H. / Sandy, J. / Sanchez-Weatherby, J. / Budziszewski, G.R. / Hough, M.A. / Bowman, S.E.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM141273 United States
CitationJournal: Biorxiv / Year: 2025
Title: Does crossing the pond affect crystal quality?
Authors: Campomizzi, C.S. / Snell, M.E. / Mikolajek, H. / Sandy, J. / Sanchez-Weatherby, J. / Budziszewski, G.R. / Russi, S. / Howells Jr., R. / Cohen, A. / Hough, M.A. / Bowman, S.E.J.
History
DepositionJun 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 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)14,3542
Polymers14,3311
Non-polymers231
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.668, 78.668, 37.683
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-324-

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 / Details: monomer / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.03 Å3/Da / Density % sol: 39.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.78 M sodium chloride, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 293 K / Ambient temp details: ambient temperature / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: VMXi / Wavelength: 0.7749 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Oct 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.57→55.6 Å / Num. obs: 17048 / % possible obs: 99.8 % / Redundancy: 15.8 % / CC1/2: 1 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.023 / Rrim(I) all: 0.075 / Net I/σ(I): 20.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.6-55.6314.90.021704810.0060.021
1.57-1.641.1537960.4280.841.436

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
MOLREPphasing
Cootmodel building
xia2.multiplexdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→55.6 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.745 / SU ML: 0.059 / Cross valid method: FREE R-VALUE / ESU R: 0.076 / ESU R Free: 0.083
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2033 839 4.933 %
Rwork0.1616 16170 -
all0.164 --
obs-17009 99.742 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.171 Å2
Baniso -1Baniso -2Baniso -3
1--0.124 Å2-0 Å2-0 Å2
2---0.124 Å2-0 Å2
3---0.248 Å2
Refinement stepCycle: LAST / Resolution: 1.57→55.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms980 0 1 58 1039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0111011
X-RAY DIFFRACTIONr_bond_other_d0.0010.016907
X-RAY DIFFRACTIONr_angle_refined_deg2.1981.7691373
X-RAY DIFFRACTIONr_angle_other_deg0.7881.7712077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3715132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.83357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01410159
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.2621046
X-RAY DIFFRACTIONr_chiral_restr0.1180.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021284
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02264
X-RAY DIFFRACTIONr_nbd_refined0.2730.2237
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.2854
X-RAY DIFFRACTIONr_nbtor_refined0.1940.2545
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.2606
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.4970.243
X-RAY DIFFRACTIONr_metal_ion_refined0.1630.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1620.26
X-RAY DIFFRACTIONr_nbd_other0.2320.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0620.28
X-RAY DIFFRACTIONr_mcbond_it2.6622.134522
X-RAY DIFFRACTIONr_mcbond_other2.6622.132522
X-RAY DIFFRACTIONr_mcangle_it3.783.815653
X-RAY DIFFRACTIONr_mcangle_other3.8023.821654
X-RAY DIFFRACTIONr_scbond_it4.4382.581489
X-RAY DIFFRACTIONr_scbond_other4.4342.586490
X-RAY DIFFRACTIONr_scangle_it6.7574.495719
X-RAY DIFFRACTIONr_scangle_other6.7534.499720
X-RAY DIFFRACTIONr_lrange_it7.73821.6121229
X-RAY DIFFRACTIONr_lrange_other7.7421.2361226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.6110.301560.2971143X-RAY DIFFRACTION98.3593
1.611-1.6550.311480.2671148X-RAY DIFFRACTION98.5985
1.655-1.7030.283570.2451113X-RAY DIFFRACTION99.6593
1.703-1.7550.251640.2061059X-RAY DIFFRACTION99.7336
1.755-1.8130.244520.191058X-RAY DIFFRACTION100
1.813-1.8760.259460.1761029X-RAY DIFFRACTION100
1.876-1.9470.208520.155977X-RAY DIFFRACTION100
1.947-2.0260.2490.141963X-RAY DIFFRACTION100
2.026-2.1160.164440.139908X-RAY DIFFRACTION100
2.116-2.220.182430.142881X-RAY DIFFRACTION100
2.22-2.3390.183360.137835X-RAY DIFFRACTION100
2.339-2.4810.208450.147794X-RAY DIFFRACTION100
2.481-2.6520.21390.151760X-RAY DIFFRACTION100
2.652-2.8640.2410.176689X-RAY DIFFRACTION100
2.864-3.1370.23410.156647X-RAY DIFFRACTION100
3.137-3.5050.179360.16583X-RAY DIFFRACTION100
3.505-4.0450.144290.137527X-RAY DIFFRACTION100
4.045-4.9480.192280.124461X-RAY DIFFRACTION100
4.948-6.9690.229210.168363X-RAY DIFFRACTION100
6.969-55.60.208120.204232X-RAY DIFFRACTION100

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