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- PDB-2htx: Crystal Structure Analysis of Hen Egg White Lysozyme Crosslinked ... -

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Basic information

Entry
Database: PDB / ID: 2htx
TitleCrystal Structure Analysis of Hen Egg White Lysozyme Crosslinked by Polymerized Glutaraldehyde in Acidic Environment
ComponentsLysozyme C
KeywordsHYDROLASE / Tetragonal / Crosslinked / Glutaraldehyde
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
UNDECA-3,7-DIENE-1,3,7,11-TETRACARBALDEHYDE / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.56 Å
AuthorsWine, Y. / Cohen-Hadar, N. / Freeman, A. / Lagziel-Simis, S. / Frolow, F.
CitationJournal: Biotechnol.Bioeng. / Year: 2007
Title: Elucidation of the mechanism and end products of glutaraldehyde crosslinking reaction by X-ray structure analysis
Authors: Wine, Y. / Cohen-Hadar, N. / Freeman, A. / Frolow, F.
History
DepositionJul 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)15,02311
Polymers14,3311
Non-polymers69210
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.856, 78.856, 36.954
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-9630-

HOH

21A-9657-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lysozyme C / E.C.3.2.1.17 / 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: see REMARK 400 / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme

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Non-polymers , 5 types, 125 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-220 / UNDECA-3,7-DIENE-1,3,7,11-TETRACARBALDEHYDE


Mass: 264.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H20O4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCOMPOUND UNDER ACIDIC CONDITIONS TWO LYSINE RESIDUES FROM NEIGHBORING LYSOZYME MOLECULES REACT WITH ...COMPOUND UNDER ACIDIC CONDITIONS TWO LYSINE RESIDUES FROM NEIGHBORING LYSOZYME MOLECULES REACT WITH POLYMERIC GLUTARALDEHYDE: ONE FORMS A SCHIFF BASE WITH THE ALDEHYDE MOIETY AND THE OTHER LYSINE FORMS A C-N BOND BY UNDERGOING MICHAEL-TYPE ADDITION WITH THE ADJACENT DOUBLE ETHYLENIC BOND VIA ITS ALPHA-CARBON THESE COVALENT BONDS ARE REPRESENTED BY LINK RECORDS BELOW: NZ OF LYS A 13 BINDS TO TWO CARBONS OF THE LIGAND 200, C14 IN THE SAME ASYMMETRIC UNIT AND C10 BY SYMMETRY OPERATION 8_555.

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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: 38.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1M Sodium Acetate, 7% NaCl, 25% Ethylene glycol, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 15, 2005 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.56→55.73 Å / Num. all: 17157 / Num. obs: 17157 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.036 / Rsym value: 0.036 / Net I/σ(I): 47.2
Reflection shellResolution: 1.56→1.59 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 2.34 / Rsym value: 0.367 / % possible all: 87.1

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Processing

Software
NameVersionClassification
REFMAC5.2refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.2phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: In-House Coordinates

Resolution: 1.56→55.73 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.035 / SU ML: 0.05
Isotropic thermal model: Structure was refined using Anisotropic thermal parameters
Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1824 842 5 %RANDOM
Rwork0.1266 ---
obs0.12937 15912 97.66 %-
all-17157 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.913 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.37 Å2
Refine analyzeLuzzati coordinate error obs: 0.049 Å
Refinement stepCycle: LAST / Resolution: 1.56→55.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1097 0 40 123 1260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211166
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.9251579
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7565155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61822.71259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3215199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.141515
X-RAY DIFFRACTIONr_chiral_restr0.1040.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02902
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.2607
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2817
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2103
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2890.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.6282686
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it8.3131110
X-RAY DIFFRACTIONr_scbond_it14.3445513
X-RAY DIFFRACTIONr_scangle_it16.2437458
X-RAY DIFFRACTIONr_rigid_bond_restr9.2931199
X-RAY DIFFRACTIONr_sphericity_free22.9493127
X-RAY DIFFRACTIONr_sphericity_bonded14.03331133
LS refinement shellResolution: 1.56→1.6 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 57 -
Rwork0.136 1046 -
obs--89.02 %

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