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- PDB-5wra: Crystal structure of hen egg-white lysozyme -

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Basic information

Entry
Database: PDB / ID: 5wra
TitleCrystal structure of hen egg-white lysozyme
ComponentsLysozyme C
KeywordsHYDROLASE / XFEL / SFX
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
Lysozyme - #10 / 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 / Lysozyme-like domain superfamily ...Lysozyme - #10 / 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 / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / FOURIER SYNTHESIS / Resolution: 1.45 Å
AuthorsSugahara, M. / Suzuki, M. / Masuda, T. / Inoue, S. / Nango, E.
CitationJournal: Sci Rep / Year: 2017
Title: Hydroxyethyl cellulose matrix applied to serial crystallography
Authors: Sugahara, M. / Nakane, T. / Masuda, T. / Suzuki, M. / Inoue, S. / Song, C. / Tanaka, R. / Nakatsu, T. / Mizohata, E. / Yumoto, F. / Tono, K. / Joti, Y. / Kameshima, T. / Hatsui, T. / ...Authors: Sugahara, M. / Nakane, T. / Masuda, T. / Suzuki, M. / Inoue, S. / Song, C. / Tanaka, R. / Nakatsu, T. / Mizohata, E. / Yumoto, F. / Tono, K. / Joti, Y. / Kameshima, T. / Hatsui, T. / Yabashi, M. / Nureki, O. / Numata, K. / Nango, E. / Iwata, S.
History
DepositionDec 1, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)14,3903
Polymers14,3311
Non-polymers582
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area6590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.600, 79.600, 38.300
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-1124-

HOH

21A-1147-

HOH

31A-1183-

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: UNP residues 19-147
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 41.89 %
Crystal growTemperature: 299 K / Method: batch mode / Details: sodium chloride, PEG 6000, pH 3.0

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Data collection

DiffractionMean temperature: 299 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 0.95 Å
DetectorType: MPCCD / Detector: CCD / Date: Apr 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 22415 / % possible obs: 100 % / Redundancy: 945 % / Net I/σ(I): 13.4

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
CrystFELdata processing
CrystFELdata scaling
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.45→26.075 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.09
RfactorNum. reflection% reflection
Rfree0.1963 1144 5.11 %
Rwork0.1805 --
obs0.1813 22371 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→26.075 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 2 83 1085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071024
X-RAY DIFFRACTIONf_angle_d1.0711379
X-RAY DIFFRACTIONf_dihedral_angle_d12.978364
X-RAY DIFFRACTIONf_chiral_restr0.048144
X-RAY DIFFRACTIONf_plane_restr0.005180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.5160.26551500.24762569X-RAY DIFFRACTION100
1.516-1.59590.22161390.20552615X-RAY DIFFRACTION100
1.5959-1.69590.20511560.18182594X-RAY DIFFRACTION100
1.6959-1.82680.18471370.17732625X-RAY DIFFRACTION100
1.8268-2.01060.18621490.16722637X-RAY DIFFRACTION100
2.0106-2.30140.18111260.1642657X-RAY DIFFRACTION100
2.3014-2.89890.20211490.18422687X-RAY DIFFRACTION100
2.8989-26.07880.19541380.18252843X-RAY DIFFRACTION100

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