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- PDB-5v8g: Pekin duck lysozyme isoform I (DEL-I) -

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Basic information

Entry
Database: PDB / ID: 5v8g
TitlePekin duck lysozyme isoform I (DEL-I)
Componentslysozyme isoform I
KeywordsHYDROLASE / lysozyme / N-acetylmuramidase
Function / homology
Function and homology information


lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / extracellular region
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
THIOCYANATE ION / Lysozyme C-1 / :
Similarity search - Component
Biological speciesAnas platyrhynchos (mallard)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
Model detailsPekin duck lysozyme isoform I (DEL-I)
AuthorsLangley, D.B. / Christ, D.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Structural basis of antigen recognition: crystal structure of duck egg lysozyme.
Authors: Langley, D.B. / Crossett, B. / Schofield, P. / Jackson, J. / Zeraati, M. / Maltby, D. / Christie, M. / Burnett, D. / Brink, R. / Goodnow, C. / Christ, D.
History
DepositionMar 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / 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.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 9, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: lysozyme isoform I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2513
Polymers14,1581
Non-polymers942
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-13 kcal/mol
Surface area6340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.200, 65.400, 31.640
Angle α, β, γ (deg.)90.000, 113.240, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein lysozyme isoform I / DEL-I


Mass: 14157.944 Da / Num. of mol.: 1 / Fragment: UNP residues 19-145 / Source method: isolated from a natural source / Source: (natural) Anas platyrhynchos (mallard) / References: UniProt: U3J0P1, UniProt: P00705*PLUS
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 115 / 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: 1.89 Å3/Da / Density % sol: 35.04 % / Description: plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 200 mM potassium thiocyanate, 100 mM Bis-Tris-propane, pH 8.5, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.2→32.7 Å / Num. obs: 30531 / % possible obs: 93.5 % / Redundancy: 4.7 % / Biso Wilson estimate: 9.9 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.041 / Rrim(I) all: 0.09 / Net I/σ(I): 10.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.2-1.224.30.4810.8470.2550.54788.6
6.58-32.74.10.060.9880.0330.06944

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.2 Å15.9 Å
Translation4.84 Å15.9 Å

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Processing

Software
NameVersionClassification
MOSFLMdata collection
Aimless0.5.17data scaling
PHASER2.5.7phasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IEE

1iee


Resolution: 1.2→32.7 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.429 / SU ML: 0.029 / SU R Cruickshank DPI: 0.0439 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.044 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1803 1613 5.3 %RANDOM
Rwork0.145 ---
obs0.1468 28891 93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 90.78 Å2 / Biso mean: 15.336 Å2 / Biso min: 6.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20.16 Å2
2--0.9 Å20 Å2
3----0.94 Å2
Refinement stepCycle: final / Resolution: 1.2→32.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms966 0 4 115 1085
Biso mean--23.28 29.1 -
Num. residues----127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021013
X-RAY DIFFRACTIONr_bond_other_d0.0020.02882
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.911376
X-RAY DIFFRACTIONr_angle_other_deg1.07132032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0965130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59122.76647
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.11915159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3111511
X-RAY DIFFRACTIONr_chiral_restr0.1080.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021170
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02233
X-RAY DIFFRACTIONr_rigid_bond_restr1.88531895
X-RAY DIFFRACTIONr_sphericity_free35.426582
X-RAY DIFFRACTIONr_sphericity_bonded9.54151905
LS refinement shellResolution: 1.202→1.233 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 129 -
Rwork0.241 2039 -
all-2168 -
obs--88.96 %

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