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- PDB-1ljg: CRYSTAL STRUCTURE OF MONOCLINIC LYSOZYME GROWN IN PRESENCE OF 5% ... -

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Basic information

Entry
Database: PDB / ID: 1ljg
TitleCRYSTAL STRUCTURE OF MONOCLINIC LYSOZYME GROWN IN PRESENCE OF 5% GLYCEROL
ComponentsLysozyme C
KeywordsHYDROLASE / Hydration of Proteins
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: 1.9 Å
AuthorsSaraswathi, N.T. / Sankaranarayanan, R. / Vijayan, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Effect of stabilizing additives on the structure and hydration of proteins: a study involving monoclinic lysozyme.
Authors: Saraswathi, N.T. / Sankaranarayanan, R. / Vijayan, M.
#1: 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.
#2: 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.
History
DepositionApr 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 16, 2024Group: 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: Lysozyme C
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0969
Polymers28,6622
Non-polymers4347
Water5,567309
1
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5174
Polymers14,3311
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5795
Polymers14,3311
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.857, 62.714, 60.019
Angle α, β, γ (deg.)90.00, 90.42, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein Lysozyme C / 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.: 2 / 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.: 7 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 1.83 Å3/Da / Density % sol: 32.75 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 4.6
Details: Sodium Acetate(0.1M)-Buffer, Sodium Nitrate (0.44M)-Precipitant, glycerol(0.54M) - Additive; pH 4.6, LIQUID DIFFUSION at 293K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 Msodium acetate11pH4.6
25 %glycerol11

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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. obs: 15576 / Biso Wilson estimate: 17.8 Å2
Reflection shellResolution: 1.9→1.97 Å
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 15695 / % possible obs: 95.8 % / Num. measured all: 61157 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 93.9 % / Num. unique obs: 1520 / Rmerge(I) obs: 0.12

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
CNS0.4refinement
RefinementResolution: 1.9→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 571549.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1237 7.9 %RANDOM
Rwork0.205 ---
obs0.205 15576 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 77.2201 Å2 / ksol: 0.370338 e/Å3
Displacement parametersBiso mean: 20.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å20 Å2-1.82 Å2
2---1.76 Å20 Å2
3----0.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.04 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 28 309 2339
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_d23.3
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: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 191 7.6 %
Rwork0.23 2317 -
obs--92.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3NITRATE.PARAMNITRATE.TOP
Refinement
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7
LS refinement shell
*PLUS
Rfactor Rwork: 0.23

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