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- PDB-1iiz: Crystal Structure of the Induced Antibacterial Protein from Tasar... -

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Basic information

Entry
Database: PDB / ID: 1iiz
TitleCrystal Structure of the Induced Antibacterial Protein from Tasar Silkworm, Antheraea mylitta
ComponentsLYSOZYME
KeywordsHYDROLASE
Function / homology
Function and homology information


cytolysis / metabolic process / lysozyme / lysozyme activity / defense response to bacterium
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 speciesAntheraea mylitta (butterflies/moths)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJain, D. / Nair, D.T. / Swaminathan, G.J. / Abraham, E.G. / Nagaraju, J. / Salunke, D.M.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Structure of the induced antibacterial protein from tasar silkworm, Antheraea mylitta. Implications to molecular evolution.
Authors: Jain, D. / Nair, D.T. / Swaminathan, G.J. / Abraham, E.G. / Nagaraju, J. / Salunke, D.M.
History
DepositionApr 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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


Theoretical massNumber of molelcules
Total (without water)13,7611
Polymers13,7611
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.985, 51.700, 94.664
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein LYSOZYME /


Mass: 13761.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Antheraea mylitta (butterflies/moths) / References: UniProt: Q7SID7, lysozyme
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.33 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 Macetate1reservoirpH5.5
226.5 %PEG80001reservoir

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Data collection

Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionBiso Wilson estimate: 16.8 Å2
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 4807 / % possible obs: 98.7 % / Rmerge(I) obs: 0.083

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LMN

1lmn


Resolution: 2.4→100 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 227924.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.283 449 10.4 %RANDOM
Rwork0.231 ---
obs-4298 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.88 Å2 / ksol: 0.644 e/Å3
Displacement parametersBiso mean: 22.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2---3.65 Å20 Å2
3---4.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.4→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms961 0 0 58 1019
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it5.261.5
X-RAY DIFFRACTIONc_mcangle_it8.162
X-RAY DIFFRACTIONc_scbond_it5.712
X-RAY DIFFRACTIONc_scangle_it8.352.5
LS refinement shellResolution: 2.4→2.54 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.307 71 10.4 %
Rwork0.291 611 -
obs--92.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 10.4 % / Rfactor obs: 0.238 / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77
X-RAY DIFFRACTIONc_mcbond_it5.261.5
X-RAY DIFFRACTIONc_scbond_it5.712
X-RAY DIFFRACTIONc_mcangle_it8.162
X-RAY DIFFRACTIONc_scangle_it8.352.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.307 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.291

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