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- PDB-1lzr: STRUCTURAL CHANGES OF THE ACTIVE SITE CLEFT AND DIFFERENT SACCHAR... -

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Basic information

Entry
Database: PDB / ID: 1lzr
TitleSTRUCTURAL CHANGES OF THE ACTIVE SITE CLEFT AND DIFFERENT SACCHARIDE BINDING MODES IN HUMAN LYSOZYME CO-CRYSTALLIZED WITH HEXA-N-ACETYL-CHITOHEXAOSE AT PH 4.0
ComponentsHUMAN LYSOZYME
KeywordsHYDROLASE (O-GLYCOSYL)
Function / homology
Function and homology information


metabolic process / cytolysis / antimicrobial humoral response / retina homeostasis / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / lysozyme / lysozyme activity / tertiary granule lumen ...metabolic process / cytolysis / antimicrobial humoral response / retina homeostasis / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / lysozyme / lysozyme activity / tertiary granule lumen / 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 C / 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 C / 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 / Lysozyme C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsMatsushima, M. / Inaka, K.
CitationJournal: J.Mol.Biol. / Year: 1994
Title: Structural changes of active site cleft and different saccharide binding modes in human lysozyme co-crystallized with hexa-N-acetyl-chitohexaose at pH 4.0.
Authors: Song, H. / Inaka, K. / Maenaka, K. / Matsushima, M.
History
DepositionSep 14, 1994Processing site: BNL
Revision 1.0Apr 20, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / 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_assembly_gen / struct_asym / struct_conn / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: HUMAN LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6224
Polymers14,7211
Non-polymers9023
Water2,936163
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.510, 60.910, 34.010
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 HUMAN LYSOZYME


Mass: 14720.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00695, UniProt: P61626*PLUS, lysozyme
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 830.786 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.12 %
Crystal grow
*PLUS
Temperature: 13 ℃ / pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
21.4 mg/ml1drop(GlcNAc)4
330 mMsodium phosphate1drop
42.5 M1dropNaCl

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 9999 Å / Num. obs: 17996 / % possible obs: 92.3 % / Num. measured all: 64767 / Rmerge(I) obs: 0.029
Reflection shell
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 1.53 Å / % possible obs: 87.6 %

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.5→5 Å /
RfactorNum. reflection
obs0.14 17500
Refinement stepCycle: LAST / Resolution: 1.5→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1029 0 59 163 1251
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0340.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.050.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.1411.5
X-RAY DIFFRACTIONp_mcangle_it1.6942
X-RAY DIFFRACTIONp_scbond_it2.1762
X-RAY DIFFRACTIONp_scangle_it3.4912.5
X-RAY DIFFRACTIONp_plane_restr0.0150.02
X-RAY DIFFRACTIONp_chiral_restr0.1490.15
X-RAY DIFFRACTIONp_singtor_nbd0.1750.3
X-RAY DIFFRACTIONp_multtor_nbd0.1760.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1810.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.13
X-RAY DIFFRACTIONp_staggered_tor13.715
X-RAY DIFFRACTIONp_orthonormal_tor22.320
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
LS refinement shell
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 1.6 Å / Rfactor obs: 0.17

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