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- PDB-1lzn: NEUTRON STRUCTURE OF HEN EGG-WHITE LYSOZYME -

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Basic information

Entry
Database: PDB / ID: 1lzn
TitleNEUTRON STRUCTURE OF HEN EGG-WHITE LYSOZYME
ComponentsPROTEIN (LYSOZYME)
KeywordsHYDROLASE
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
DEUTERATED WATER / NITRATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodNEUTRON DIFFRACTION / MOLECULAR REPLACEMEN XPLOR / Resolution: 1.7 Å
AuthorsBon, C.I. / Lehmann, M.S. / Wilkinson, C.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Quasi-Laue neutron-diffraction study of the water arrangement in crystals of triclinic hen egg-white lysozyme.
Authors: Bon, C. / Lehmann, M.S. / Wilkinson, C.
#1: Journal: Physica B (AMSTERDAM) / Year: 1998
Title: Neutron Laue Diffraction in Macromolecular Crystallography
Authors: Myles, D.A.A. / Bon, C. / Langan, P. / Cipriani, F. / Castagna, J.C. / Lehmann, M.S. / Wilkinson, C.
History
DepositionMar 23, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Apr 1, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Jun 30, 2021Group: Data collection / Derived calculations
Category: diffrn_detector / diffrn_radiation ...diffrn_detector / diffrn_radiation / diffrn_radiation_wavelength / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _diffrn_detector.detector / _diffrn_radiation.pdbx_diffrn_protocol ..._diffrn_detector.detector / _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _diffrn_radiation.pdbx_scattering_type / _diffrn_source.pdbx_wavelength / _diffrn_source.pdbx_wavelength_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (LYSOZYME)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6647
Polymers14,3311
Non-polymers3336
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.280, 32.040, 34.270
Angle α, β, γ (deg.)88.80, 108.80, 111.60
Int Tables number1
Space group name H-MP1

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Components

#1: Protein PROTEIN (LYSOZYME)


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NITRATE IONS PRESENT / Source: (natural) Gallus gallus (chicken) / Cell: EGG / Cellular location: CYTOPLASM (WHITE) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 1.82 Å3/Da / Density % sol: 31.82 %
Description: EXCHANGEABLE HYDROGENS (LABIL HYDROGENS+HYDROGENS WITHIN THE SOLVENT) WERE REPLACED BY DEUTERIUM. SITES OF EXCHANGEABLE HYDROGEN ON THE PROTEIN WERE ALL NAMED D*, AND WERE ASSIGNED THE ...Description: EXCHANGEABLE HYDROGENS (LABIL HYDROGENS+HYDROGENS WITHIN THE SOLVENT) WERE REPLACED BY DEUTERIUM. SITES OF EXCHANGEABLE HYDROGEN ON THE PROTEIN WERE ALL NAMED D*, AND WERE ASSIGNED THE SCATTERING LENGTH OF DEUTERIUM. WHEN THE HYDROGEN IS ACTUALLY EXCHANGED BY DEUTERIUM, THE OCCUPANCY IS 1, AND WHEN IT IS ACTUALLY NOT EXCHANGED,THE OCCUPANCY IS -0.56. PART OF SITES OF HYDRATION WERE MODELIZED AS COMPLETE D2O ENTITIES (MOLECULE DOD), AND PART OF THEM WERE MODELIZED AS SINGLE OXYGEN ATOM (MOLECULE HOH), BECAUSE OF DYNAMICAL DISORDER.
Crystal growpH: 4.7
Details: BATCH TECHNIQUE EQUAL AMOUNT OF 1.0 % SOLUTION OF HEN EGG-WHITE LYSOZYME ( BOEHRINGER) AND 2.8 % NANO3 IN 50 MM ACETATE BUFFER (PH 4.7)
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.0 %protein11
22.8 %11NaNO3
350 mMacetate11

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceWavelength: 2.7-3.5
DetectorDetector: IMAGE PLATE / Date: Dec 1, 1997
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
12.71
23.51
ReflectionResolution: 1.7→13.6 Å / Num. obs: 8976 / % possible obs: 83 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.146 / Rsym value: 0.114 / Net I/σ(I): 35
Reflection
*PLUS
Observed criterion σ(F): 2 / Num. measured all: 46061

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Processing

Software
NameVersionClassification
CCP4LAUE SUITE MODIFIED FOR CYLINDER GEOMETRY (C. WILKINSON)refinement
CCP4LAUE SUITEdata reduction
X-PLOR3.1refinement
CCP4(LAUE SUITE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMEN XPLOR
Starting model: PDB ENTRY 4LZT

4lzt


Resolution: 1.7→13.6 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: POSITIONS OF NON HYDROGEN ATOMS OF THE PROTEIN WERE KEPT FROM 4LZT, BECAUSE NEUTRON REFINEMENT CAN'T PROVIDE BETTER POSITIONS . WE BETTER FOCUSED OUR ATTENTION ON MODELING HYDROGEN AND HYDRATION SITES
RfactorNum. reflection% reflectionSelection details
Rfree0.221 471 5 %RANDOM
Rwork0.204 ---
obs-8976 83 %-
Displacement parametersBiso mean: 17.82 Å2
Refinement stepCycle: LAST / Resolution: 1.7→13.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 21 243 1265
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONx_bond_d0.016
NEUTRON DIFFRACTIONx_bond_d_na
NEUTRON DIFFRACTIONx_bond_d_prot
NEUTRON DIFFRACTIONx_angle_d
NEUTRON DIFFRACTIONx_angle_d_na
NEUTRON DIFFRACTIONx_angle_d_prot
NEUTRON DIFFRACTIONx_angle_deg0.033
NEUTRON DIFFRACTIONx_angle_deg_na
NEUTRON DIFFRACTIONx_angle_deg_prot
NEUTRON DIFFRACTIONx_dihedral_angle_d
NEUTRON DIFFRACTIONx_dihedral_angle_d_na
NEUTRON DIFFRACTIONx_dihedral_angle_d_prot
NEUTRON DIFFRACTIONx_improper_angle_d
NEUTRON DIFFRACTIONx_improper_angle_d_na
NEUTRON DIFFRACTIONx_improper_angle_d_prot
NEUTRON DIFFRACTIONx_mcbond_it
NEUTRON DIFFRACTIONx_mcangle_it
NEUTRON DIFFRACTIONx_scbond_it
NEUTRON DIFFRACTIONx_scangle_it
Xplor fileSerial no: 1 / Param file: PARALLH22X.PRO / Topol file: TOPALLH22X
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 13.6 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS

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