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- PDB-2z2e: Crystal Structure of Canine Milk Lysozyme Stabilized against Non-... -

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Basic information

Entry
Database: PDB / ID: 2z2e
TitleCrystal Structure of Canine Milk Lysozyme Stabilized against Non-enzymatic Deamidation
ComponentsLysozyme C, milk isozyme
KeywordsHYDROLASE / LYSOZYME C / Milk Lysozyme / 1 / 4-BETA-N-Acetylmuramidase C / Bacteriolytic enzyme
Function / homology
Function and homology information


metabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium / metal ion binding
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
Lysozyme C, milk isozyme
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsNonaka, Y. / Akieda, D. / Watanabe, N. / Tanaka, I. / Kamiya, M. / Aizawa, T. / Nitta, K. / Demura, M. / Kawano, K.
CitationJournal: Proteins / Year: 2008
Title: Spontaneous asparaginyl deamidation of canine milk lysozyme under mild conditions
Authors: Nonaka, Y. / Aizawa, T. / Akieda, D. / Yasui, M. / Watanabe, M. / Watanabe, N. / Tanaka, I. / Kamiya, M. / Mizuguchi, M. / Demura, M. / Kawano, K.
History
DepositionMay 21, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C, milk isozyme
B: Lysozyme C, milk isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3134
Polymers29,1212
Non-polymers1922
Water3,873215
1
A: Lysozyme C, milk isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6572
Polymers14,5611
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lysozyme C, milk isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6572
Polymers14,5611
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.216, 31.216, 198.307
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Lysozyme C, milk isozyme / 1 / 4-beta-N-acetylmuramidase C


Mass: 14560.574 Da / Num. of mol.: 2 / Mutation: N44Q/N47Q/N49Q/N68Q/N103Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris / Plasmid: pPIC3 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P81708, lysozyme
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 1.92 Å3/Da / Density % sol: 35.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 10mM sodium citrate, 1M ammonium sulfate, 5% ethylene glycol, 2.5% iso-propanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. all: 14424 / Num. obs: 14193 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.023 Å2 / Net I/σ(I): 25.927
Reflection shellResolution: 2.01→2.08 Å / Mean I/σ(I) obs: 11.992

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CWI

2cwi


Resolution: 2.01→27.04 Å / Cor.coef. Fo:Fc: 0.847 / Cor.coef. Fo:Fc free: 0.679 / SU B: 9.44 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.41266 682 5 %RANDOM
Rwork0.27264 ---
obs0.2795 12996 95.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.382 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.05 Å20 Å2
2---0.09 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.01→27.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 10 215 2255
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.032
X-RAY DIFFRACTIONr_angle_refined_deg2.774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.916
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.94
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.091
X-RAY DIFFRACTIONr_chiral_restr0.208
X-RAY DIFFRACTIONr_gen_planes_refined0.013
X-RAY DIFFRACTIONr_nbd_refined0.3
X-RAY DIFFRACTIONr_nbtor_refined0.319
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.395
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.422
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.477
X-RAY DIFFRACTIONr_mcbond_it1.368
X-RAY DIFFRACTIONr_mcangle_it2.021
X-RAY DIFFRACTIONr_scbond_it3.66
X-RAY DIFFRACTIONr_scangle_it4.774
LS refinement shellResolution: 2.013→2.066 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.484 57 -
Rwork0.314 956 -
obs--92.17 %

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