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- PDB-5vas: Pekin duck egg lysozyme isoform III (DEL-III), orthorhombic form -

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Basic information

Entry
Database: PDB / ID: 5vas
TitlePekin duck egg lysozyme isoform III (DEL-III), orthorhombic form
ComponentsLysozyme
KeywordsHYDROLASE / duck lysozyme / glycosyl hydrolase / N-acetylmuramidase
Function / homologyLysozyme - #10 / Lysozyme / Orthogonal Bundle / Mainly Alpha / PHOSPHATE ION / :
Function and homology information
Biological speciesAnas platyrhynchos (mallard)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
Model detailsPekin duck lysozyme isoform I (DEL-I)
AuthorsChristie, M. / Christ, D. / Langley, D.B.
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 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / 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
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,00310
Polymers29,2572
Non-polymers7458
Water4,882271
1
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0956
Polymers14,6291
Non-polymers4665
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9084
Polymers14,6291
Non-polymers2793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.005, 58.350, 107.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lysozyme


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, lysozyme
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.36 Å3/Da / Density % sol: 47.94 % / Description: plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.4 M ammonium phosphate monobasic, 100 mM Tris, pH 8.5

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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: Mar 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.4→27.78 Å / Num. obs: 55408 / % possible obs: 100 % / Redundancy: 14.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.024 / Rrim(I) all: 0.094 / Net I/σ(I): 17.8 / Num. measured all: 803682 / Scaling rejects: 2920
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.4-1.4214.10.9120.8480.2490.946100
7.67-27.7812.10.0340.9990.010.03597.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata collection
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IEE

1iee


Resolution: 1.4→27.78 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.875 / SU ML: 0.033 / SU R Cruickshank DPI: 0.0571 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.052 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1693 2763 5 %RANDOM
Rwork0.1438 ---
obs0.1451 52574 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 54.3 Å2 / Biso mean: 15.243 Å2 / Biso min: 6.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2---0.23 Å20 Å2
3---0.94 Å2
Refinement stepCycle: final / Resolution: 1.4→27.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 45 271 2328
Biso mean--29.64 29.87 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022182
X-RAY DIFFRACTIONr_bond_other_d0.0020.022007
X-RAY DIFFRACTIONr_angle_refined_deg1.41.932967
X-RAY DIFFRACTIONr_angle_other_deg1.02234569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2615278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.44421.887106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.86715358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3771531
X-RAY DIFFRACTIONr_chiral_restr0.0940.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022545
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02570
X-RAY DIFFRACTIONr_rigid_bond_restr0.90234189
X-RAY DIFFRACTIONr_sphericity_free27.5885177
X-RAY DIFFRACTIONr_sphericity_bonded4.8754234
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 207 -
Rwork0.226 3821 -
all-4028 -
obs--99.9 %
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)
11.1796-0.13030.60480.7393-0.02531.541500.1010.026-0.10840.0155-0.0096-0.10080.0536-0.01550.0665-0.00540.00960.01160.00070.00287.0175-7.4643-9.1325
21.29460.26910.50652.98340.4861.8293-0.04040.06330.05130.01860.054-0.08590.0220.0933-0.01370.06840.01030.01370.0174-0.00370.02-5.671816.021-12.5245
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 129
2X-RAY DIFFRACTION2B1 - 129

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