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- PDB-1ljn: Crystal Structure of Turkey Egg Lysozyme Complex with Di-N-acetyl... -

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Basic information

Entry
Database: PDB / ID: 1ljn
TitleCrystal Structure of Turkey Egg Lysozyme Complex with Di-N-acetylchitobiose at 1.19A Resolution
Componentslysozyme C
KeywordsHYDROLASE / sugar complex / non-productive binding
Function / homology
Function and homology information


glycosaminoglycan binding / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / extracellular space / identical protein binding / cytoplasm
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 speciesMeleagris gallopavo (turkey)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsHarata, K. / Kanai, R.
CitationJournal: Proteins / Year: 2002
Title: Crystallographic dissection of the thermal motion of protein-sugar complex.
Authors: Harata, K. / Kanai, R.
History
DepositionApr 22, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 28, 2021Group: Structure summary / Category: chem_comp / struct / Item: _chem_comp.pdbx_synonyms / _struct.title
Revision 2.2Oct 25, 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

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Assembly

Deposited unit
A: lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8454
Polymers14,2281
Non-polymers6173
Water3,171176
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.200, 33.290, 46.210
Angle α, β, γ (deg.)90.00, 109.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein lysozyme C


Mass: 14228.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Meleagris gallopavo (turkey) / References: UniProt: P00703, lysozyme
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 176 / 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: 1.94 Å3/Da / Density % sol: 36.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.2
Details: ammonium sulfate, pH 4.2, VAPOR DIFFUSION, temperature 293K
Crystal grow
*PLUS
Method: batch method / Details: Harata, K., (1993) Acta Crystallogr., D49, 497.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 %aqueous 1-propanol solution11
2100 mgTEL11
33 Mammonium sulfate11

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Data collection

DiffractionMean temperature: 286 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: ENRAF-NONIUS FAST / Detector: AREA DETECTOR / Date: Nov 19, 1999 / Details: graphite monochromator
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.19→15.8 Å / Num. all: 35242 / Num. obs: 32310 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.21 % / Rmerge(I) obs: 0.052
Reflection shellResolution: 1.19→1.21 Å / Rmerge(I) obs: 0.206 / % possible all: 49.1
Reflection
*PLUS
Num. obs: 32432 / % possible obs: 92 % / Num. measured all: 103984

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Processing

Software
NameClassification
MADNESSdata collection
MERGEFdata reduction
X-PLORmodel building
SHELXL-97refinement
MADNESSdata reduction
MERGEFdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LZY

1lzy


Resolution: 1.19→15.8 Å / Isotropic thermal model: Anisotropic U / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: For some water molecules, it can not be distinguished if the sites are occupied by one molecule or two, and thus the occupancies of the alternate conformations are greater than 1.00. For ...Details: For some water molecules, it can not be distinguished if the sites are occupied by one molecule or two, and thus the occupancies of the alternate conformations are greater than 1.00. For example, in HOH 238, occupancy(A)+occupancy(B)=1, occupancy(A)+occupancy(C)=1, and occupancy(B)=ocupancy(C).
RfactorNum. reflection% reflectionSelection details
Rfree0.138 1621 5 %random
Rwork0.103 ---
all0.104 32432 --
obs0.104 32432 --
Displacement parametersBiso mean: 14 Å2
Refinement stepCycle: LAST / Resolution: 1.19→15.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1011 0 40 208 1259
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.012
X-RAY DIFFRACTIONs_approx_iso_adps0.052
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.049
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rwork: 0.104
Solvent computation
*PLUS
Displacement parameters
*PLUS

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