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- PDB-1lks: HEN EGG WHITE LYSOZYME NITRATE -

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Basic information

Entry
Database: PDB / ID: 1lks
TitleHEN EGG WHITE LYSOZYME NITRATE
ComponentsLYSOZYME
KeywordsHYDROLASE / GLYCOSIDASE / LYSOZYME
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: 1.1 Å
AuthorsSteinrauf, L.K.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structures of monoclinic lysozyme iodide at 1.6 A and of triclinic lysozyme nitrate at 1.1 A.
Authors: Steinrauf, L.K.
#1: 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.
#2: Journal: Acta Crystallogr.,Sect.C / Year: 1983
Title: Studies of Monoclinic Hen Egg White Lysozyme. II. The Refinement at 2.5 A Resolution--Conformational Variability between the Two Independent Molecules
Authors: Rao, S.T. / Hogle, J. / Sundaralingam, M.
#3: Journal: Acta Crystallogr. / Year: 1959
Title: Preliminary X-Ray Data for Some New Crystalline Forms of Beta-Lactoglobulin and Hen Egg-White Lysozyme
Authors: Steinrauf, L.K.
History
DepositionOct 9, 1997Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 26, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_conn / struct_ncs_oper / struct_site / symmetry
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_conn.pdbx_leaving_atom_flag / _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 / _symmetry.Int_Tables_number / _symmetry.space_group_name_H-M
Details: strict ncs operation x, y+1/2, z+1/2 added to support update from space group #1 setting A 1 to more widely recognized setting P 1
Provider: repository / Type: Remediation
Revision 1.4Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_PDB_caveat / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7037
Polymers14,3311
Non-polymers3726
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.970, 65.080, 27.250
Angle α, β, γ (deg.)94.57, 111.56, 82.98
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(1), (1), (1)-1.02995, 31.81881, 12.66271

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Components

#1: Protein LYSOZYME / MURAMIDASE


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / 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.: 197 / 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: 1.82 Å3/Da / Density % sol: 26 %
Crystal growDetails: THE CRYSTALS WERE GROWN IN THE PRESENCE OF BROMO PHENYL BLUE (BPB), AND THE CRYSTALS WERE DARK BLUE, ALMOST BLACK. HOWEVER, NO RELIABLE TRACE OF THE BPB WAS FOUND.
Crystal
*PLUS
Crystal grow
*PLUS
pH: 4.7 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMacetate11
210 mg/mlprotein12
35 %(w/w)sodium iodide12

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 15, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.1→20 Å / Num. obs: 36397 / % possible obs: 78.8 % / Redundancy: 4 % / Rmerge(I) obs: 0.095
Reflection
*PLUS
Num. measured all: 216397

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Processing

Software
NameVersionClassification
MSCSOFTWAREdata collection
MSCSOFTWAREdata reduction
SHELXL-93model building
SHELXL-93refinement
MSCdata scaling
SHELXL-93phasing
RefinementResolution: 1.1→20 Å / Cross valid method: FREE R / σ(F): 1
Details: WATER MOLECULES 272, 333, AND 319, HAVE NO REASONABLE PROTEIN CONTACTS AND MAY BE PART OF THE UNRESOLVED BROMO PHENOL BLUE DISORDER.
Num. reflection% reflectionSelection details
all36397 --
obs-78.8 %-
Rfree--RANDOM
Refinement stepCycle: LAST / Resolution: 1.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1038 0 189 24 1251
Software
*PLUS
Name: SHELXL-93 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.1101 / Rfactor obs: 0.0989 / Rfactor Rfree: 0.1416
Solvent computation
*PLUS
Displacement parameters
*PLUS

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