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- PDB-5v94: Pekin duck egg lysozyme isoform III (DEL-III), cubic form -

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Basic information

Entry
Database: PDB / ID: 5v94
TitlePekin duck egg lysozyme isoform III (DEL-III), cubic form
Componentslysozyme isoform III
KeywordsHYDROLASE / lysozyme / glycosyl hydrolase / N-acetylmuramidase
Function / homology
Function and homology information


metabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to 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
PHOSPHATE ION / Lysozyme C-1 / :
Similarity search - Component
Biological speciesAnas platyrhynchos (mallard)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 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 III
B: lysozyme isoform III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,16211
Polymers29,2572
Non-polymers9059
Water2,756153
1
A: lysozyme isoform III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3448
Polymers14,6291
Non-polymers7157
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: lysozyme isoform III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8193
Polymers14,6291
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.950, 95.950, 95.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-201-

PO4

21A-204-

PO4

31B-202-

PO4

41B-202-

PO4

51A-302-

HOH

61A-415-

HOH

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Components

#1: Protein lysozyme isoform III / DEL-III


Mass: 14628.607 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Anas platyrhynchos (mallard) / Tissue: egg white
References: UniProt: U3J0P1, UniProt: P00705*PLUS, exo-alpha-sialidase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.52 Å3/Da / Density % sol: 51.11 % / Description: cubic
Crystal growTemperature: 293 K / Method: evaporation / pH: 8.8
Details: 100 mM ammonium phosphate dibasic, 100 mM Tris, pH 8.8, 45% MPD

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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: 1.65→42.91 Å / Num. obs: 35458 / % possible obs: 99.9 % / Redundancy: 20.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.023 / Rrim(I) all: 0.103 / Net I/σ(I): 18.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.65-1.6818.51.0153340318040.8610.2411.0432.7100
8.9-42.9117.30.0541252390.9990.0130.05239.990.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.65 Å30.34 Å
Translation1.65 Å30.34 Å

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Processing

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

1iee


Resolution: 1.65→30.34 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.125 / SU ML: 0.054 / SU R Cruickshank DPI: 0.0931 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.092 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2143 1747 4.9 %RANDOM
Rwork0.1872 ---
obs0.1885 33669 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 77.3 Å2 / Biso mean: 26 Å2 / Biso min: 11.92 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.65→30.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 0 51 153 2162
Biso mean--39.95 32.82 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022067
X-RAY DIFFRACTIONr_bond_other_d0.0020.021809
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.9362815
X-RAY DIFFRACTIONr_angle_other_deg1.07934146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3665262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16922.66790
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.97415317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5491521
X-RAY DIFFRACTIONr_chiral_restr0.0980.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022335
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02466
LS refinement shellResolution: 1.653→1.696 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 118 -
Rwork0.222 2471 -
all-2589 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9012-0.4716-0.20041.5199-0.19780.67640.005-0.0433-0.0272-0.0042-0.0357-0.0210.0310.03080.03080.00870.00130.01090.04540.01440.0194-25.8987-12.2431-1.7689
21.82220.5521-1.44810.4036-0.3561.56380.08970.0920.2137-0.021-0.018-0.0157-0.1884-0.0162-0.07170.061-0.01350.00320.06010.03630.1018-9.705414.15046.0742
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 129
2X-RAY DIFFRACTION2B1 - 129

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