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- PDB-7der: Lysozyme alone in H2O -

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Basic information

Entry
Database: PDB / ID: 7der
TitleLysozyme alone in H2O
ComponentsLysozyme C
KeywordsHYDROLASE
Function / homology
Function and homology information


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 Gram-positive bacterium / defense response to bacterium ...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 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: 1.03 Å
AuthorsTanaka, I. / Chatake, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H05436 Japan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Recent structural insights into the mechanism of lysozyme hydrolysis.
Authors: Tanaka, I. / Nishinomiya, R. / Goto, R. / Shimazaki, S. / Chatake, T.
History
DepositionNov 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)14,4966
Polymers14,3311
Non-polymers1655
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-24 kcal/mol
Surface area6580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.777, 78.777, 37.093
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-357-

HOH

21A-369-

HOH

31A-521-

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-CL / CHLORIDE ION / Chloride


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


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


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.01 Å3/Da / Density % sol: 38.74 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 15mg/mL lysozyme, 0.7M NaCl in a buffer of 50mM sodium-acetate (pH4.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.03→33.559 Å / Num. obs: 58098 / % possible obs: 99.97 % / Redundancy: 12.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.8
Reflection shellResolution: 1.03→1.056 Å / Rmerge(I) obs: 0.728 / Num. unique obs: 3926 / CC1/2: 0.915

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wld

4wld


Resolution: 1.03→33.559 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1733 2000 3.44 %
Rwork0.1487 --
obs0.1495 58098 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.03→33.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 5 233 1239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061067
X-RAY DIFFRACTIONf_angle_d1.121449
X-RAY DIFFRACTIONf_dihedral_angle_d11.926394
X-RAY DIFFRACTIONf_chiral_restr0.052153
X-RAY DIFFRACTIONf_plane_restr0.004191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.03-1.05580.22091400.20753926X-RAY DIFFRACTION100
1.0558-1.08430.17791410.18063937X-RAY DIFFRACTION100
1.0843-1.11620.21341410.16183980X-RAY DIFFRACTION100
1.1162-1.15230.17561400.14863935X-RAY DIFFRACTION100
1.1523-1.19340.18021420.14533972X-RAY DIFFRACTION100
1.1934-1.24120.17511420.14133964X-RAY DIFFRACTION100
1.2412-1.29770.14991410.13623961X-RAY DIFFRACTION100
1.2977-1.36610.17081410.13613979X-RAY DIFFRACTION100
1.3661-1.45170.17061430.12963988X-RAY DIFFRACTION100
1.4517-1.56380.16641420.12663998X-RAY DIFFRACTION100
1.5638-1.72120.15171430.1284023X-RAY DIFFRACTION100
1.7212-1.97020.161460.14844060X-RAY DIFFRACTION100
1.9702-2.48210.17571450.15344095X-RAY DIFFRACTION100
2.4821-33.5590.18011530.15684280X-RAY DIFFRACTION100

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