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- PDB-7vei: Neutron structure of D2O-solvent lysozyme -

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Basic information

Entry
Database: PDB / ID: 7vei
TitleNeutron structure of D2O-solvent lysozyme
ComponentsLysozyme C
KeywordsHYDROLASE / hydrolase D2O solution neutron diffraction D/H contrast
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
DEUTERATED WATER / NICKEL (II) ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodNEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChatake, T. / Tanaka, I. / Kusaka, K. / Fujiwara, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16K05014 Japan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Protonation states of hen egg-white lysozyme observed using D/H contrast neutron crystallography.
Authors: Chatake, T. / Tanaka, I. / Kusaka, K. / Fujiwara, S.
History
DepositionSep 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)14,4253
Polymers14,3311
Non-polymers942
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.140, 79.140, 37.779
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-325-

DOD

21A-351-

DOD

31A-388-

DOD

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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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: D2O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 4.5
Details: 15-25mg/mL HEWL, 50mM sodium acetate (pH4.5), 0.1g/mL NiCl2

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SPALLATION SOURCE / Site: JPARC MLF / Beamline: BL-03 / Type: J-PARC MLF BEAMLINE BL-03 / Wavelength: 2.3-6.8
DetectorType: iBIX / Detector: DIFFRACTOMETER / Date: Jun 2, 2019
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
12.31
26.81
ReflectionResolution: 1.8→17.7 Å / Num. obs: 11376 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3674 % / CC1/2: 0.9818 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.0712 / Net I/σ(I): 6.53
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.9338 % / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 1.06 / Num. unique obs: 1072 / CC1/2: 0.6705 / Rpim(I) all: 0.2843 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIX1.18.1_3865refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7FCU
Resolution: 2→17.7 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / Phase error: 18.25
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.215 840 10.01 %
Rwork0.1701 20901 -
obs0.1745 8392 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0082201
NEUTRON DIFFRACTIONf_angle_d1.0413847
NEUTRON DIFFRACTIONf_chiral_restr0.099148
NEUTRON DIFFRACTIONf_plane_restr0.022442
NEUTRON DIFFRACTIONf_dihedral_angle_d16.3555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.130.21551340.17091207NEUTRON DIFFRACTION98
2.13-2.290.21331360.16111225NEUTRON DIFFRACTION98
2.29-2.520.20371390.15131253NEUTRON DIFFRACTION100
2.52-2.880.19621410.17341263NEUTRON DIFFRACTION100
2.88-3.630.23961410.17411279NEUTRON DIFFRACTION99
3.63-17.70.21211490.17621325NEUTRON DIFFRACTION97

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