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- PDB-4xad: Crystal structure of hen egg white lysozyme in complex with Galf-... -

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Basic information

Entry
Database: PDB / ID: 4xad
TitleCrystal structure of hen egg white lysozyme in complex with Galf-GlcNAc
ComponentsLysozyme C
KeywordsHYDROLASE / galactofuranose / Galf-GlcNAc / protein-carbohydrate complex / Trypanosoma cruzi O-linked disaccharide
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / 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 ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / 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 / defense response to bacterium / endoplasmic reticulum / 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 speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å
AuthorsWangkanont, K. / Kiessling, L.L.
CitationJournal: to be published
Title: Crystal structure of hen egg white lysozyme in complex with Galf-GlcNAc, an O-linked disaccharide core from Trypanosoma cruzi
Authors: Wangkanont, K. / Kiessling, L.L.
History
DepositionDec 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_nat / pdbx_struct_assembly ...entity_src_nat / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact / software / struct_keywords
Item: _entity_src_nat.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details ..._entity_src_nat.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_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_asym_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.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: 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)14,9278
Polymers14,3311
Non-polymers5967
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-56 kcal/mol
Surface area6450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.002, 78.002, 37.709
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-350-

HOH

21A-415-

HOH

Detailsbiological unit is the same as asym.

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: egg white / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Polysaccharide beta-D-galactofuranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalfb1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-4]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(4+1)][b-D-Galf]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2 Å3/Da / Density % sol: 38.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 100 mM NaOAc, 1.5 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97904 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 5, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 1.25→30.4 Å / Num. obs: 32700 / % possible obs: 99.5 % / Redundancy: 28 % / Biso Wilson estimate: 12.99 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.017 / Rrim(I) all: 0.09 / Χ2: 1.266 / Net I/av σ(I): 50.286 / Net I/σ(I): 11.8 / Num. measured all: 914067
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.25-1.2924.50.49230940.9620.0990.5020.67295.5
1.29-1.3528.10.38432100.9830.0730.3910.729100
1.35-1.4128.30.28532270.9890.0540.290.82100
1.41-1.4828.40.21332200.9940.040.2170.922100
1.48-1.5728.50.16532760.9960.0310.1671.085100
1.57-1.728.70.13832570.9960.0260.141.368100
1.7-1.8728.70.10932620.9980.0210.1111.428100
1.87-2.1428.80.09132910.9980.0170.0921.703100
2.14-2.6928.60.08233500.9980.0160.0841.913100
2.69-30.426.90.07535130.9980.0150.0771.84399.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.07 Å27.11 Å
Translation5.07 Å27.11 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.5.2phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 194L

194l


Resolution: 1.25→27.11 Å / FOM work R set: 0.933 / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 12.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1681 2975 4.85 %
Rwork0.1402 58361 -
obs0.1414 -99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 50.4 Å2 / Biso mean: 17.11 Å2 / Biso min: 7.93 Å2
Refinement stepCycle: final / Resolution: 1.25→27.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 32 190 1223
Biso mean--15.19 27.86 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051163
X-RAY DIFFRACTIONf_angle_d1.0131577
X-RAY DIFFRACTIONf_chiral_restr0.072166
X-RAY DIFFRACTIONf_plane_restr0.003208
X-RAY DIFFRACTIONf_dihedral_angle_d14.145476
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2492-1.29390.19323070.15735597590495
1.2939-1.34570.15873420.136157886130100
1.3457-1.40690.16813210.123958486169100
1.4069-1.48110.17542910.12458296120100
1.4811-1.57390.1293040.111359236227100
1.5739-1.69540.15372980.116258626160100
1.6954-1.86590.16463060.131558356141100
1.8659-2.13590.16142750.136458726147100
2.1359-2.69060.17082760.149859046180100
2.6906-27.11590.17962550.151459036158100

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