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- PDB-5lym: STUDIES OF MONOCLINIC HEN EGG WHITE LYSOZYME. IV. X-RAY REFINEMEN... -

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Basic information

Entry
Database: PDB / ID: 5lym
TitleSTUDIES OF MONOCLINIC HEN EGG WHITE LYSOZYME. IV. X-RAY REFINEMENT AT 1.8 ANGSTROM RESOLUTION AND A COMPARISON OF THE VARIABLE REGIONS IN THE POLYMORPHIC FORMS
ComponentsLYSOZYME
KeywordsHYDROLASE (O-GLYCOSYL)
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
NITRATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsRao, S.T. / Sundaralingam, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Studies of monoclinic hen egg-white lysozyme. IV. X-ray refinement at 1.8 A resolution and a comparison of the variable regions in the polymorphic forms.
Authors: Rao, S.T. / Sundaralingam, M.
#1: Journal: To be Published
Title: X-Ray Refinement Studies on Monoclinic Hel Containing Two Independent Molecules at 1.8 Angstrom Resolution
Authors: Yu, C. / Rao, S.T. / Sundaralingam, M.
#2: Journal: Acta Crystallogr.,Sect.C / Year: 1983
Title: Studies of Monoclinic Hen Egg White Lysozyme. II. The Refinement at 2.5 Angstroms Resolution-Conformational Variability between the Two Independent Molecules
Authors: Rao, S.T. / Hogle, J. / Sundaralingam, M.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1981
Title: Studies of Monoclinic Hen Egg White Lysozyme. I. Structure Solution at 4 Angstroms Resolution and Molecular-Packing Comparisons with Tetragonal and Triclinic Lysozymes
Authors: Hogle, J. / Rao, S.T. / Mallikarjunan, M. / Beddell, C. / Mcmullan, R.K. / Sundaralingam, M.
#4: Journal: Thesis / Year: 1978
Title: The Structure of the Monoclinic Crystal Form of Hen Egg White Lysozyme at 2.5 Angstroms Resolution. Comparison of a Protein Structure in Several Crystalline Environments
Authors: Hogle, J.
History
DepositionJul 20, 1995Processing site: BNL
SupersessionOct 15, 1995ID: 1LYM
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LYSOZYME
B: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0348
Polymers28,6622
Non-polymers3726
Water2,000111
1
A: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5174
Polymers14,3311
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5174
Polymers14,3311
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.000, 62.500, 60.900
Angle α, β, γ (deg.)90.00, 90.80, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9738, -0.1931, 0.1201), (0.2055, 0.9734, -0.1017), (-0.0972, 0.1237, 0.9875)
Vector: -14.38, 4.35, -31.36)

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Components

#1: Protein LYSOZYME


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


Mass: 62.005 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 1.86 Å3/Da / Density % sol: 33.82 %
Crystal grow
*PLUS
Method: other / Details: Hogle, J., (1981) Acta Cryst., B37, 591.

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: BRUKER NONIUS CAD4 / Detector: DIFFRACTOMETER
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→8 Å / Num. obs: 18822 / % possible obs: 99 %
Reflection
*PLUS
Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
X-PLOR3phasing
RefinementResolution: 1.8→8 Å / σ(F): 3
RfactorNum. reflection% reflection
Rfree0.264 --
Rwork0.189 --
obs0.189 17524 93 %
Displacement parametersBiso mean: 19.2 Å2
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 24 111 2137
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.2

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