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- PDB-1lkr: MONOCLINIC HEN EGG WHITE LYSOZYME IODIDE -

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Basic information

Entry
Database: PDB / ID: 1lkr
TitleMONOCLINIC HEN EGG WHITE LYSOZYME IODIDE
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
IODIDE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 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
DepositionJan 20, 1998Processing 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 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / refine / 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 / _refine.pdbx_starting_model / _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: LYSOZYME
B: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,82019
Polymers28,6622
Non-polymers2,15717
Water5,603311
1
A: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,72712
Polymers14,3311
Non-polymers1,39611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0937
Polymers14,3311
Non-polymers7616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.894, 63.153, 60.227
Angle α, β, γ (deg.)90.00, 90.12, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.975515, 0.165171, -0.14522), (-0.15195, 0.983525, 0.097923), (0.159001, -0.073459, 0.984542)
Vector: 12.82347, -2.73238, 31.97197)

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Components

#1: Protein LYSOZYME / MURAMIDASE


Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: WORTHINGTON BIOCHEMICALS, USED WITHOUT PURIFICATION
Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 26 %
Crystal growpH: 8
Details: 1% PROTEIN, 200 MMOLAR ACETATE BUFFER, PH 8, 5% SODIUM IODIDE, pH 8.0
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMacetate11
21.0 Msodium hydroxide11
310 mg/mlprotein11
45 %(w/w)sodium iodide11

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 1, 1994
RadiationMonochromator: BENT CYLINDRICAL GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→8 Å / Num. obs: 22327 / % possible obs: 63 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.0761
Reflection
*PLUS
Num. measured all: 68962

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Processing

Software
NameClassification
MCSdata reduction
X-PLORmodel building
X-PLORrefinement
MCSdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→8 Å / Cross valid method: FREE R / σ(F): 1 / Stereochemistry target values: ENGH AND HUBER
Details: REFINEMENT WAS INITIATED BY PROLSQ, WHICH DID NOT ALLOW ANISOTROPY. THE FINAL REFINEMENT WAS CARRIED OUT USING SHELX-L93 WITH ALL ATOMS ANISOTROPIC. THE PRESENCE OF THE 17 IODIDE ATOMS MAKES ...Details: REFINEMENT WAS INITIATED BY PROLSQ, WHICH DID NOT ALLOW ANISOTROPY. THE FINAL REFINEMENT WAS CARRIED OUT USING SHELX-L93 WITH ALL ATOMS ANISOTROPIC. THE PRESENCE OF THE 17 IODIDE ATOMS MAKES THE APPLICATION OF THE USUAL ANALYSIS OF ERRORS NOT VALID. ONLY WHEN ANOTHER MONOCLINIC LYSOZYME STRUCTURE WITHOUT HEAVY ATOMS HAS BEEN REFINED BY THE SAME PROCEDURE WILL AN ANALYSIS BE POSSIBLE. NEVERTHELESS, A COMPARISON OF THE BOND LENGTHS BETWEEN THE TWO MOLECULES OF LYSOZYME GIVES AN AVERAGE ERROR OF 0.12 ANGSTROMS, WHICH IS IN GOOD AGREEMENT WITH THE LUZATTI ANALYSIS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1404 4369 10 %RANDOM
all0.1058 44071 --
obs0.1404 -63 %-
Refine analyzeNum. disordered residues: 0
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 17 296 2315
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_similar_dist0.002
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol0.159
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.094
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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