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- PDB-5lsh: human lysozyme in complex with a tetrasaccharide fragment of the ... -

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Basic information

Entry
Database: PDB / ID: 5lsh
Titlehuman lysozyme in complex with a tetrasaccharide fragment of the O-chain of LPS from Klebsiella pneumoniae
ComponentsLysozyme C
KeywordsSUGAR BINDING PROTEIN / lectin / complex / LPS / O-chain
Function / homology
Function and homology information


antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism ...antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / inflammatory response / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.061 Å
AuthorsZhang, R. / Nifantiev, N.E. / Krylov, V. / Luetteke, T. / Scheidig, A.J. / Siebert, H.-C.
CitationJournal: Q. Rev. Biophys. / Year: 2017
Title: Lysozyme's lectin-like characteristics facilitates its immune defense function.
Authors: Zhang, R. / Wu, L. / Eckert, T. / Burg-Roderfeld, M. / Rojas-Macias, M.A. / Lutteke, T. / Krylov, V.B. / Argunov, D.A. / Datta, A. / Markart, P. / Guenther, A. / Norden, B. / Schauer, R. / ...Authors: Zhang, R. / Wu, L. / Eckert, T. / Burg-Roderfeld, M. / Rojas-Macias, M.A. / Lutteke, T. / Krylov, V.B. / Argunov, D.A. / Datta, A. / Markart, P. / Guenther, A. / Norden, B. / Schauer, R. / Bhunia, A. / Enani, M.A. / Billeter, M. / Scheidig, A.J. / Nifantiev, N.E. / Siebert, H.C.
History
DepositionAug 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_struct_conn_angle / struct_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.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.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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 C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5596
Polymers14,7211
Non-polymers8385
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-22 kcal/mol
Surface area6930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.108, 56.040, 60.531
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14720.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LYZ, LZM / Production host: Mus musculus (house mouse) / References: UniProt: P61626, lysozyme
#2: Polysaccharide alpha-D-galactopyranose-(1-3)-beta-D-galactofuranose-(1-3)-alpha-D-galactopyranose-(1-3)-propyl ...alpha-D-galactopyranose-(1-3)-beta-D-galactofuranose-(1-3)-alpha-D-galactopyranose-(1-3)-propyl beta-D-galactofuranoside


Type: oligosaccharide / Mass: 708.658 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,4,3/[a2112h-1b_1-4_1*OCCC][a2112h-1a_1-5][a2112h-1b_1-4]/1-2-3-2/a3-b1_b3-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][propyl]{[(1+1)][b-D-Galf]{[(3+1)][a-D-Galp]{[(3+1)][b-D-Galf]{[(3+1)][a-D-Galp]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 1.91 Å3/Da / Density % sol: 35.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.8 M NaCl, 25 mM NaOAc, pH 5.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.061→30.265 Å / Num. obs: 47721 / % possible obs: 92 % / Redundancy: 11.9 % / Biso Wilson estimate: 9.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.072 / Net I/σ(I): 17.06
Reflection shellResolution: 1.061→1.099 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 1.52 / CC1/2: 0.633 / % possible all: 69

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1REX

1rex


Resolution: 1.061→30.265 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.07
RfactorNum. reflection% reflection
Rfree0.2032 2372 5 %
Rwork0.1801 --
obs0.1813 47421 91.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.061→30.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1029 0 52 160 1241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131288
X-RAY DIFFRACTIONf_angle_d1.5691773
X-RAY DIFFRACTIONf_dihedral_angle_d27.705544
X-RAY DIFFRACTIONf_chiral_restr0.105205
X-RAY DIFFRACTIONf_plane_restr0.009220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.061-1.08270.3208830.34181579X-RAY DIFFRACTION55
1.0827-1.10620.3481300.30072479X-RAY DIFFRACTION87
1.1062-1.1320.27141330.262528X-RAY DIFFRACTION89
1.132-1.16030.26981350.23852560X-RAY DIFFRACTION90
1.1603-1.19170.26891380.2282625X-RAY DIFFRACTION92
1.1917-1.22670.24891410.21732670X-RAY DIFFRACTION93
1.2267-1.26630.23831400.2112664X-RAY DIFFRACTION93
1.2663-1.31160.22241410.19792673X-RAY DIFFRACTION94
1.3116-1.36410.21981430.19212694X-RAY DIFFRACTION94
1.3641-1.42620.19491440.18662735X-RAY DIFFRACTION95
1.4262-1.50140.19551420.17412758X-RAY DIFFRACTION95
1.5014-1.59540.20771450.16972742X-RAY DIFFRACTION95
1.5954-1.71860.22371460.16752778X-RAY DIFFRACTION96
1.7186-1.89150.18791460.18232784X-RAY DIFFRACTION96
1.8915-2.16520.19821510.16912831X-RAY DIFFRACTION96
2.1652-2.72760.20381520.17112873X-RAY DIFFRACTION97
2.7276-30.27780.16941620.15763076X-RAY DIFFRACTION99

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