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- PDB-1rcm: CRYSTAL STRUCTURE OF A UBIQUITIN-DEPENDENT DEGRADATION SUBSTRATE:... -

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Basic information

Entry
Database: PDB / ID: 1rcm
TitleCRYSTAL STRUCTURE OF A UBIQUITIN-DEPENDENT DEGRADATION SUBSTRATE: A THREE-DISULFIDE FORM OF LYSOZYME
ComponentsHEN EGG WHITE LYSOZYME
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
ACETIC ACID / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsHill, C.P. / Johnston, N.L. / Cohen, R.E.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Crystal structure of a ubiquitin-dependent degradation substrate: a three-disulfide form of lysozyme.
Authors: Hill, C.P. / Johnston, N.L. / Cohen, R.E.
#1: Journal: J.Biol.Chem. / Year: 1991
Title: Specific Disulfide Cleavage is Required for Ubiquitin Conjugation and Degradation of Lysozyme
Authors: Dunten, R.L. / Cohen, R.E. / Gregori, L. / Chau, V.
History
DepositionJan 10, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 15, 2020Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_distant_solvent_atoms ...pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_conn
Item: _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: HEN EGG WHITE LYSOZYME
B: HEN EGG WHITE LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7824
Polymers28,6622
Non-polymers1202
Water2,396133
1
A: HEN EGG WHITE LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3912
Polymers14,3311
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HEN EGG WHITE LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3912
Polymers14,3311
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.700, 81.300, 38.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES CYS A 127 AND CYS B 127 ARE CARBOXYMETHYLATED.

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Components

#1: Protein HEN EGG WHITE LYSOZYME


Mass: 14331.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.09 Å3/Da / Density % sol: 41.25 %
Crystal grow
*PLUS
pH: 3.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
19 mg/mlprotein1drop
27 %1reservoirNaCl
350 mMsodium acetate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 10 Å / Num. obs: 18295 / % possible obs: 93.8 % / Rmerge F obs: 0.185

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.185 / Rfactor obs: 0.185 / Highest resolution: 1.9 Å
Details: THE DISULFIDE BETWEEN RESIDUES 6 AND 127 HAS BEEN REDUCED AND CARBOXYMETHYLATED. THE CARBOXYMETHYL GROUP BOUND TO CYS 6 COULD NOT BE LOCATED DURING THE CRYSTALLOGRAPHIC ANALYSIS AND IS NOT ...Details: THE DISULFIDE BETWEEN RESIDUES 6 AND 127 HAS BEEN REDUCED AND CARBOXYMETHYLATED. THE CARBOXYMETHYL GROUP BOUND TO CYS 6 COULD NOT BE LOCATED DURING THE CRYSTALLOGRAPHIC ANALYSIS AND IS NOT INCLUDED IN THE COORDINATE FILE. THE CARBOXYMETHYL GROUP BOUND TO CYS 127 IS PRESENTED AS HET GROUP ACT 127 AT THE END OF THE CHAIN.
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 8 133 2143
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refinement
*PLUS
Highest resolution: 1.9 Å / Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.8

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