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- PDB-1lmn: THE REFINED CRYSTAL STRUCTURE OF LYSOZYME FROM THE RAINBOW TROUT ... -

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Basic information

Entry
Database: PDB / ID: 1lmn
TitleTHE REFINED CRYSTAL STRUCTURE OF LYSOZYME FROM THE RAINBOW TROUT (ONCORHYNCHUS MYKISS)
ComponentsRAINBOW TROUT LYSOZYME
KeywordsHYDROLASE (O-GLYCOSYL)
Function / homology
Function and homology information


lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / extracellular space
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 speciesOncorhynchus mykiss (rainbow trout)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsKarlsen, S. / Hough, E.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Refined crystal structure of lysozyme from the rainbow trout (Oncorhynchus mykiss).
Authors: Karlsen, S. / Eliassen, B.E. / Hansen, L.K. / Larsen, R.L. / Riise, B.W. / Smalas, A.O. / Hough, E. / Grinde, B.
#1: Journal: Eur.J.Biochem. / Year: 1988
Title: Purification and Characterization of Two Lysozymes from Rainbow Trout (Salmo Gairdneri)
Authors: Grinde, B. / Jolles, J. / Jolles, P.
History
DepositionOct 19, 1994Processing site: BNL
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 26, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / atom_sites ...atom_site / atom_sites / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_validate_rmsd_angle / struct_conn / struct_ref_seq_dif
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _struct_conn.pdbx_dist_value / _struct_ref_seq_dif.details
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RAINBOW TROUT LYSOZYME


Theoretical massNumber of molelcules
Total (without water)14,3031
Polymers14,3031
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.680, 76.680, 54.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein RAINBOW TROUT LYSOZYME


Mass: 14303.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oncorhynchus mykiss (rainbow trout) / References: UniProt: P11941, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.93 %
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop / PH range low: 10 / PH range high: 4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 Macetate1reservoir
20.1 Mcitrate1reservoir
30.1 Mphosphate1reservoir
418 mg/mllysozyme1drop80& of typeI and 20% of type II
530-45 %satammonium sulfate1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 16305 / % possible obs: 91.2 % / Observed criterion σ(I): 3
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 42.11 Å / Num. measured all: 70573 / Rmerge(I) obs: 0.0417

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Processing

Software
NameClassification
MERLOTphasing
PROLSQrefinement
RefinementResolution: 1.8→8 Å / σ(F): 3
Details: THE STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT METHODS USING THE MERLOT PACKAGE (FITZGERALD, P. (1988) J. APPL. CRYST. 21, 273-278) AND THE REFINED MODEL OF THE HEN EGG-WHITE LYSOZYME AS ...Details: THE STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT METHODS USING THE MERLOT PACKAGE (FITZGERALD, P. (1988) J. APPL. CRYST. 21, 273-278) AND THE REFINED MODEL OF THE HEN EGG-WHITE LYSOZYME AS SEARCH MODEL (BROOKHAVEN PROTEIN DATA BANK, ENTRY 1LZT, HODSON ET AL.,(1990), ACTA. CRYST. B46, 52-62.
RfactorNum. reflection
obs0.174 16305
Displacement parametersBiso mean: 24.4 Å2
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms999 0 0 127 1126
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0440.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0470.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0130.02
X-RAY DIFFRACTIONp_chiral_restr0.0380.06
X-RAY DIFFRACTIONp_singtor_nbd0.1720.03
X-RAY DIFFRACTIONp_multtor_nbd0.2540.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2240.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor6.43
X-RAY DIFFRACTIONp_staggered_tor18.315
X-RAY DIFFRACTIONp_orthonormal_tor18.620
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS

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