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- PDB-1jj0: CRYSTAL STRUCTURE OF TETRAGONAL LYSOZYME GROWN IN PRESENCE of 30%... -

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Basic information

Entry
Database: PDB / ID: 1jj0
TitleCRYSTAL STRUCTURE OF TETRAGONAL LYSOZYME GROWN IN PRESENCE of 30% SUCROSE
ComponentsLYSOZYME
KeywordsHYDROLASE / GLYCOSIDASE / ENZYME-TETRAGONAL FORM / MUCOPEPTIDE N-ACETYLMURAMYL HYDROLASE / HEN EGG-WHITE 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
sucrose / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDatta, S. / Biswal, B.K. / Vijayan, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: The effect of stabilizing additives on the structure and hydration of proteins: a study involving tetragonal lysozyme.
Authors: Datta, S. / Biswal, B.K. / Vijayan, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Hydration, Mobility and Accessibility of Lysozyme: Strucutres of a Ph 6.5 Orthorhombic Form and its Low-Humidity Variant and a Comparative Study Involving 20 Crystallographically Independent Molecules
Authors: Biswal, B.K. / Sukumar, N. / Vijayan, M.
#2: 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, K. / Kodandapani, R. / Vijayan, M.
History
DepositionJul 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6732
Polymers14,3311
Non-polymers3421
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.006, 79.006, 38.151
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

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Components

#1: Protein LYSOZYME / E.C.3.2.1.17 / 1 / 4-BETA-N-ACETYLMURAMIDASE C / ALLERGEN GAL D 4 / GAL D IV


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Cellular location: CYTOPLASM / Tissue: EGG WHITE / References: UniProt: P00698, lysozyme
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.77 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 4.6
Details: Na-acetate buffer, pH 4.6, 10% NaCl, 30% sucrose, LIQUID DIFFUSION at 293K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
Conc.: 0.04 M / Common name: acetate / Details: pH4.6

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 9972 / Num. obs: 9892 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.3 Å2 / Rsym value: 0.062 / Net I/σ(I): 14.1
Reflection shellResolution: 1.9→1.97 Å / Num. unique all: 973 / Rsym value: 0.213 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 98.9 % / Num. measured all: 79880 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 99.9 % / Num. unique obs: 973 / Rmerge(I) obs: 0.213

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 193L

193l


Resolution: 1.9→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 657242.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1004 10.3 %RANDOM
Rwork0.194 ---
obs0.194 9730 97.5 %-
all-9972 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.7273 Å2 / ksol: 0.435457 e/Å3
Displacement parametersBiso mean: 26.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å20 Å2
2--0.73 Å20 Å2
3----1.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 23 145 1169
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.234 148 9.5 %
Rwork0.214 1413 -
obs--96.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3SUCROSE.PAR (HICCUP DATABASE)SUCROSE.TOP (HICCUP DATABASE)
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.3 % / Rfactor obs: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7
LS refinement shell
*PLUS
Rfactor Rfree: 0.234 / % reflection Rfree: 9.5 % / Rfactor Rwork: 0.214

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