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- PDB-7fg8: H/D exchanged Hen egg-white lysozyme denatured in acidic conditio... -

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Basic information

Entry
Database: PDB / ID: 7fg8
TitleH/D exchanged Hen egg-white lysozyme denatured in acidic conditions and refolded in solution
ComponentsLysozyme C
KeywordsHYDROLASE / H/D exchange / denatured and refolded
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 / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKita, A. / Morimoto, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: Mol Biotechnol. / Year: 2022
Title: Hydrogen/Deuterium Exchange Behavior During Denaturing/Refolding Processes Determined in Tetragonal Hen Egg-White Lysozyme Crystals.
Authors: Kita, A. / Morimoto, Y.
History
DepositionJul 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Apr 3, 2024Group: 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

Downloads & links

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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
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: From the previous studies
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-18 kcal/mol
Surface area6680 Å2
Unit cell
Length a, b, c (Å)79.182, 79.182, 37.906
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-372-

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.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: NACL, SODIUM ACETATE-D3, ACETIC ACID-D4

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12931N
22931N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.54
NUCLEAR REACTORORNL High Flux Isotope Reactor CG4D22.8-4.5
Detector
TypeIDDetectorDate
RIGAKU RAXIS VII1IMAGE PLATEFeb 13, 2018
MAATEL IMAGINE2IMAGE PLATEMar 19, 2018
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
22.81
34.51
Reflection

Biso Wilson estimate: 23.63 Å2 / Entry-ID: 7FG8 / Resolution: 2→100 Å

Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
858099.614.50.027167.6
7546918.50.16626.5
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsDiffraction-ID
2-2.070.088081
2-2.110.26810032

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
Refinement

SU ML: 0.1657 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 18.8759 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 6K8G

6k8g

/ Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBiso mean (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDσ(F)
2-39.59X-RAY DIFFRACTION22.410.18290.14030.1425418812485424.8999.6211.37
2-55.99NEUTRON DIFFRACTION0.26560.23287546912
Refinement stepCycle: LAST / Resolution: 2→39.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms997 0 2 86 1085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00582364
X-RAY DIFFRACTIONf_angle_d0.81664058
X-RAY DIFFRACTIONf_chiral_restr0.0542144
X-RAY DIFFRACTIONf_plane_restr0.0043468
X-RAY DIFFRACTIONf_dihedral_angle_d18.2902625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.070.1933420.1419768X-RAY DIFFRACTION96.43
2.07-2.150.1741270.1197793X-RAY DIFFRACTION99.88
2.15-2.250.1975410.1209805X-RAY DIFFRACTION100
2.25-2.370.1661510.1345785X-RAY DIFFRACTION100
2.37-2.520.1713380.1584807X-RAY DIFFRACTION100
2.52-2.710.186320.1552815X-RAY DIFFRACTION100
2.71-2.990.1769440.166794X-RAY DIFFRACTION100
2.99-3.420.1954530.153826X-RAY DIFFRACTION100
3.42-4.310.1836420.1256834X-RAY DIFFRACTION100
4.31-39.590.1809480.1333897X-RAY DIFFRACTION99.89

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