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- PDB-1uco: HEN EGG-WHITE LYSOZYME, LOW HUMIDITY FORM -

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Basic information

Entry
Database: PDB / ID: 1uco
TitleHEN EGG-WHITE LYSOZYME, LOW HUMIDITY FORM
ComponentsLYSOZYME
KeywordsHYDROLASE (O-GLYCOSYL) / ENZYME-MONOCLINIC FORM / HYDROLASE / 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 / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to bacterium ...Lactose synthesis / 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 bacterium / defense response to Gram-positive 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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsNagendra, H.G. / Sudarsanakumar, C. / Vijayan, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: An X-ray analysis of native monoclinic lysozyme. A case study on the reliability of refined protein structures and a comparison with the low-humidity form in relation to mobility and enzyme action.
Authors: Nagendra, H.G. / Sudarsanakumar, C. / Vijayan, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Protein Hydration and Water Structure: X-Ray Analysis of a Closely Packed Protein Crystal with Very Low Solvent Content
Authors: Madhusudan / Kodandapani, R. / Vijayan, M.
#2: Journal: J.Appl.Crystallogr. / Year: 1993
Title: Comparison of Radiation Induced Decay and Structure Refinement from X-Ray Data Collected from Lysozyme Crystals at Low and Ambient Temperatures
Authors: Young, A.C.M. / Dewan, J.C. / Nave, C. / Tilton, R.F.
History
DepositionDec 31, 1995Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LYSOZYME
B: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)28,6622
Polymers28,6622
Non-polymers00
Water4,792266
1
A: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.990, 62.840, 60.360
Angle α, β, γ (deg.)90.00, 90.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein LYSOZYME / HEN EGG-WHITE LYSOZYME / MUCOPEPTIDE N-ACETYLMURAMYL HYDROLASE


Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: CRYSTAL STRUCTURE OF NATIVE MONOCLINIC LYSOZYME / Source: (natural) Gallus gallus (chicken) / Cell: EGG / Cellular location: WHITE / References: UniProt: P00698, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 1.85 Å3/Da / Density % sol: 32.4 %
Crystal grow
*PLUS
pH: 4.6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 %protein11
22 %11NaNO3
3sodium acetate11

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jan 9, 1991
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 12993 / % possible obs: 86.6 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.0538
Reflection
*PLUS
Highest resolution: 2 Å / Rmerge(I) obs: 0.053

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Processing

Software
NameClassification
XENGENdata collection
PROLSQrefinement
XENGENdata reduction
RefinementResolution: 2→10 Å / σ(F): 4 /
RfactorNum. reflection
Rwork0.169 -
obs-12816
Displacement parametersBiso mean: 14.53 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1995 0 0 266 2261
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0410.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.1891
X-RAY DIFFRACTIONp_mcangle_it1.9261.5
X-RAY DIFFRACTIONp_scbond_it1.631
X-RAY DIFFRACTIONp_scangle_it2.6071.5
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.0050.02
X-RAY DIFFRACTIONp_singtor_nbd0.1930.5
X-RAY DIFFRACTIONp_multtor_nbd0.2980.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2180.5
X-RAY DIFFRACTIONp_planar_tor2.95
X-RAY DIFFRACTIONp_staggered_tor21.620
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor20.120
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS

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