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- PDB-6k8g: H/D exchanged Hen egg-white lysozyme -

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Basic information

Entry
Database: PDB / ID: 6k8g
TitleH/D exchanged Hen egg-white lysozyme
ComponentsLysozyme C
KeywordsHYDROLASE / H/D exchanged protein
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 / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKita, A. / Morimoto, Y.
Funding support Japan, 3items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
Other privateThe Research Development Program of Kyoto University Japan
Other privateThe Towa Foundation for Food Science & Research Japan
CitationJournal: J.Appl.Crystallogr. / Year: 2020
Title: Hydrogen/deuterium exchange behavior in tetragonal hen egg-white lysozyme crystals affected by solution state.
Authors: Kita, A. / Morimoto, Y.
History
DepositionJun 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Apr 3, 2024Group: 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)14,3903
Polymers14,3311
Non-polymers582
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-20 kcal/mol
Surface area6650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.094, 79.094, 37.828
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Components on special symmetry positions
IDModelComponents
11A-333-

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.: 87 / 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 DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: NaCl, sodium acetate-d3, acetic acid-d4, 100% D2O

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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
RIGAKU1IMAGE PLATEFeb 13, 2018
MAATEL IMAGINE2IMAGE PLATESep 20, 2018
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1CuKaSINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
22.81
34.51
Reflection

Entry-ID: 6K8G

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Biso Wilson estimate2)Rmerge(I) obsRpim(I) allRrim(I) allDiffraction-IDNet I/σ(I)
2-100805193.325.223.640.0580.0110.059163.5
2-34.12733887.86.40.1630.0590.17425.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allDiffraction-ID% possible all
2-2.07220.11526.25500.0240.118165.7
2-2.115.10.293.19470.1190.315279.5

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
PHENIX1.17_3644refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
Refinement

SU ML: 0.1571 / R Free selection details: 1 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 18.7301 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 193L

Resolution (Å)Refine-IDBiso mean2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDσ(F)
2-34.13X-RAY DIFFRACTION23.260.17980.13190.134239780264.9593.4611.44
2-34.12NEUTRON DIFFRACTION0.25540.22516477338587.72
Refinement stepCycle: LAST / Resolution: 2→34.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms997 0 2 87 1086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01322388
X-RAY DIFFRACTIONf_angle_d1.32014071
X-RAY DIFFRACTIONf_chiral_restr0.1031144
X-RAY DIFFRACTIONf_plane_restr0.0152468
X-RAY DIFFRACTIONf_dihedral_angle_d17.6318627
NEUTRON DIFFRACTIONf_bond_d0.01322388
NEUTRON DIFFRACTIONf_angle_d1.32014071
NEUTRON DIFFRACTIONf_chiral_restr0.1031144
NEUTRON DIFFRACTIONf_plane_restr0.0152468
NEUTRON DIFFRACTIONf_dihedral_angle_d17.6318627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.280.16621170.10962263X-RAY DIFFRACTION85.4
2.29-2.880.17341230.14832595X-RAY DIFFRACTION96.14
2.88-34.130.18611570.13032771X-RAY DIFFRACTION98.49

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