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- PDB-2b5z: Hen lysozyme chemically glycosylated -

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Basic information

Entry
Database: PDB / ID: 2b5z
TitleHen lysozyme chemically glycosylated
ComponentsLysozyme C
KeywordsHYDROLASE / chemical glycosylation
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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
AZIDE ION / (1S)-1,5-anhydro-1-(ethylsulfonyl)-D-glucitol / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLopez-Jaramillo, F.J. / Perez-Balderas, F. / Hernandez-Mateo, F. / Santoyo-Gonzalez, F.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Production, crystallization and X-ray characterization of chemically glycosylated hen egg-white lysozyme.
Authors: Lopez-Jaramillo, F.J. / Perez-Banderas, F. / Hernandez-Mateo, F. / Santoyo-Gonzalez, F.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Production, crystallization and X-ray characterization of chemically glycosylated hen egg-white lysozyme
Authors: Lopez-Jaramillo, F.J. / Perez-Balderas, F. / Hernandez-Mateo, F. / Santoyo-Gonzalez, F.
History
DepositionSep 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 23, 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
Revision 1.6Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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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)15,5749
Polymers14,3311
Non-polymers1,2438
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.580, 32.970, 120.270
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 / Allergen Gal d 4 / Gal d IV


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hen egg / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Sugar
ChemComp-BGS / (1S)-1,5-anhydro-1-(ethylsulfonyl)-D-glucitol / BETA-D-GLUCOPYRANOSYLSULFONYLETHANE


Type: D-saccharide / Mass: 256.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H16O7S
#3: Chemical ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: N3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.03 Å3/Da / Density % sol: 38.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: Magnesium Sulfate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 22, 2004 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.51→19.57 Å / Num. obs: 19330 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.17 % / Biso Wilson estimate: 19.2 Å2 / Limit h max: 19 / Limit h min: 0 / Limit k max: 21 / Limit k min: 0 / Limit l max: 79 / Limit l min: 0 / Observed criterion F max: 939492.49 / Observed criterion F min: 3.804 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 22.19
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 5.08 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 6.78 / Num. unique all: 2774 / Rsym value: 0.25 / % possible all: 79.6

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Processing

Software
NameVersionClassificationNB
CNS1refinement
ProDCdata collection
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IEE
Resolution: 1.6→9.88 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0.98 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1643 10 %RANDOM
Rwork0.212 ---
all-16709 --
obs-16449 98.4 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 65.3983 Å2 / ksol: 0.546683 e/Å3
Displacement parametersBiso max: 50.73 Å2 / Biso mean: 20.58 Å2 / Biso min: 9.38 Å2
Baniso -1Baniso -2Baniso -3
1--3.63 Å20 Å20 Å2
2--5.05 Å20 Å2
3----1.43 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
nonpolymerX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.1 Å
Luzzati d res high-1.6
Refinement stepCycle: LAST / Resolution: 1.6→9.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms989 0 79 80 1148
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_torsion_deg22.1
X-RAY DIFFRACTIONc_torsion_impr_deg2.16
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it1.922
X-RAY DIFFRACTIONc_scbond_it2.222
X-RAY DIFFRACTIONc_scangle_it3.122.5
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.6-1.660.24117810.80.24714380.0181643161698.4
1.66-1.720.2171589.60.2214400.0171640159897.4
1.72-1.80.22716710.10.2314610.0181657162898.2
1.8-1.90.216162100.21614550.0171623161799.6
1.9-2.010.2121428.60.2114900.0181655163298.6
2.01-2.170.21417410.40.21114720.0161666164698.8
2.17-2.380.2121619.60.20915040.0171681166599
2.38-2.720.2091609.60.20814970.0161660165799.8
2.72-3.40.20518510.80.20415260.0151716171199.7
3.4-9.880.2141568.70.21315230.0171795167993.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3ligand_xplor.parligand_xplor.top
X-RAY DIFFRACTION4AGS.parAGS.top
X-RAY DIFFRACTION5water.paramwater.top

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