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- PDB-2hu1: Crystal structure Analysis of Hen Egg White Lyszoyme -

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Basic information

Entry
Database: PDB / ID: 2hu1
TitleCrystal structure Analysis of Hen Egg White Lyszoyme
ComponentsLysozyme C
KeywordsHYDROLASE / Tetragonal / Crosslinked / Glutaraldehyde
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
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: 1.63 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: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Apr 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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)15,23219
Polymers14,3311
Non-polymers90018
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Lysozyme C
hetero molecules

A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,46338
Polymers28,6622
Non-polymers1,80136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6450 Å2
ΔGint-215 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.827, 78.827, 37.053
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-9130-

220

21A-9702-

EDO

31A-9755-

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, 99 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#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 / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCOMPOUND IN ALKALINE PH, CROSSLINKING BY POLYMERIC GLUTARALDEHYDE IS AFFECTED BY TWO LYSINE ...COMPOUND IN ALKALINE PH, CROSSLINKING BY POLYMERIC GLUTARALDEHYDE IS AFFECTED BY TWO LYSINE RESIDUES: ONE FORMING A SCHIFF BASE WITH THE ALDEHYDE MOIETY AND THE OTHER FORMING C-N BOND BY UNDERGOING MICHAEL-TYPE ADDITION WITH THE ADJACENT DOUBLE ETHYLENIC BOND VIA ITS BETA-CARBON.

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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: 2.01 Å3/Da / Density % sol: 38.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1M Sodium Acetate pH 4.8, 7% NaCl, 25% Ethylene glycol, 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: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2006 / 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: 1.629→55.73 Å / Num. all: 15141 / Num. obs: 15141 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 25.14 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 10.2
Reflection shellResolution: 1.629→1.66 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.869 / Mean I/σ(I) obs: 2.81 / Rsym value: 0.869 / % possible all: 100

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Processing

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

Resolution: 1.63→55.73 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.843 / SU ML: 0.06 / Isotropic thermal model: Used Anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2203 758 5 %RANDOM
Rwork0.14679 ---
obs0.15021 14342 99.78 %-
all-15100 --
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: 30.484 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.135 Å
Refinement stepCycle: LAST / Resolution: 1.63→55.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 44 81 1126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211112
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2751.9211494
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.755139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95822.10557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7115187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8921516
X-RAY DIFFRACTIONr_chiral_restr0.0960.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02851
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2470.2610
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2760
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.267
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.020.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3210.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1853653
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.78751046
X-RAY DIFFRACTIONr_scbond_it7.497492
X-RAY DIFFRACTIONr_scangle_it9.80910442
X-RAY DIFFRACTIONr_rigid_bond_restr4.13331145
X-RAY DIFFRACTIONr_sphericity_free12.758394
X-RAY DIFFRACTIONr_sphericity_bonded8.23331086
LS refinement shellResolution: 1.629→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 53 -
Rwork0.158 1047 -
obs--99.64 %

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